************************************************************** Software list using 2015-2019 build system ************************************************************** ---------------------------------------------------------------------------------------------------------------------------------------- The following is a list of the modules and extensions currently available: ---------------------------------------------------------------------------------------------------------------------------------------- ABAQUS: ABAQUS/6.14.2-linux-x86_64, ABAQUS/2017-hotfix-1721 Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA. ABINIT: ABINIT/8.0.8b-GCC-4.9.2, ABINIT/8.0.8b-GCC-4.9.3, ABINIT/8.0.8b-intel-2016.u3 ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis. ABRicate: ABRicate/0.8.7-spartan_intel-2017.u2 Mass screening of contigs for antimicrobial resistance or virulence genes. It comes bundled with multiple databases: Resfinder, CARD, ARG-ANNOT, NCBI BARRGD, NCBI, EcOH, PlasmidFinder, Ecoli_VF and VFDB. ABySS: ABySS/1.5.2-goolf-2015a, ABySS/1.9.0-goolf-2015a, ABySS/2.0.2-goolf-2015a Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler - Homepage: http://www.bcgsc.ca/platform/bioinfo/software/abyss ACTC: ACTC/1.1-intel-2016.u3 ACTC converts independent triangles into triangle strips or fans. - Homepage: https://sourceforge.net/projects/actc ADMIXTURE: ADMIXTURE/1.3.0 ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm. - Homepage: https://www.genetics.ucla.edu/software/admixture AFNI: AFNI/linux_openmp_64-intel-2016.u3-20180104, AFNI/linux_openmp_64-spartan_intel-2017.u2-20180521, ... Free software for analysis and display of FMRI data ANSYS_CFD: ANSYS_CFD/18.1, ANSYS_CFD/19.0 ANSYS computational fluid dynamics (CFD) simulation software allows you to predict, with confidence, the impact of fluid flows on your product throughout design and manufacturing as well as during end use. ANSYS renowned CFD analysis tools include the widely used and well-validated ANSYS Fluent and ANSYS CFX. ANTLR: ANTLR/2.7.7-intel-2016.u3, ANTLR/2.7.7-intel-2017.u2 ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) is a language tool that provides a framework for constructing recognizers, compilers, and translators from grammatical descriptions containing Java, C#, C++, or Python actions. ANTs: ANTs/2.2.0-goolf-2015a, ANTs/2.2.0-intel-2016.u3, ANTs/2.3.1-spartan_gcc-6.2.0 ANTs extracts information from complex datasets that include imaging. ANTs is useful for managing, interpreting and visualizing multidimensional data. APR: APR/1.5.2-GCC-4.9.2, APR/1.7.0-GCC-6.2.0, APR/1.7.0-spartan_intel-2017.u2 Apache Portable Runtime (APR) libraries. - Homepage: http://apr.apache.org/ APR-util: APR-util/1.5.4-GCC-4.9.2, APR-util/1.6.1-GCC-6.2.0, APR-util/1.6.1-spartan_intel-2017.u2 Apache Portable Runtime (APR) util libraries. - Homepage: http://apr.apache.org/ ARAGORN: ARAGORN/1.2.36-GCC-4.9.2 AST: AST/0.0.2-intel-2018.u4-Python-3.6.4 Deprecated. AST/NeeDles is used to convert between protobuf3 and srcML. ATK: ATK/2.18.0-intel-2016.u3, ATK/2.24.0-GCC-4.9.2, ATK/2.24.0-GCC-6.2.0, ATK/2.24.0-intel-2016.u3, ... ATK provides the set of accessibility interfaces that are implemented by other toolkits and applications. Using the ATK interfaces, accessibility tools have full access to view and control running applications. - Homepage: https://developer.gnome.org/ATK/stable/ ATLAS: ATLAS/3.10.1-GCC-4.9.2-LAPACK-3.5.0, ATLAS/3.10.1-GCC-5.4.0-LAPACK-3.5.0, ATLAS/3.10.1-GCC-6.2.0-LAPACK-3.5.0, ... ATLAS (Automatically Tuned Linear Algebra Software) is the application of the AEOS (Automated Empirical Optimization of Software) paradigm, with the present emphasis on the Basic Linear Algebra Subprograms (BLAS), a widely used, performance-critical, linear algebra kernel library. - Homepage: http://math-atlas.sourceforge.net ATSAS: ATSAS/2.8.0-2.el7.x86_64 ATSAS is a program suite for small-angle scattering data analysis from biological macromolecules. - Homepage: http://www.embl-hamburg.de/ExternalInfo/Research/Sax/software.html AUGUSTUS: AUGUSTUS/3.2.3-intel-2017.u2-Python-2.7.13, AUGUSTUS/3.3.2-intel-2017.u2, AUGUSTUS/3.3.3-spartan_intel-2017.u2-Python-3.6.4 AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences Albacore: Albacore/2.3.3-intel-2017.u2-Python-3.6.4 Albacore identifies DNA sequences directly from raw data, rather than utilising an intermediary stage called ‘event detection’. This upgrade enhances accuracy of the single-read sequence data, contributing to high consensus accuracy for nanopore sequence data. AlignGraph: AlignGraph/20160823-intel-2016.u3 Amber: Amber/16-GCC-6.2.0-CUDA, Amber/16-GCC-6.2.0, Amber/16-gompi-2017b-CUDA-mpi-Custom, Amber/16-gompi-2017b-CUDA-mpi Amber (originally Assisted Model Building with Energy Refinement) is software for performing molecular dynamics and structure prediction. AmberTools: AmberTools/18-spartan_intel-2017.u2, AmberTools/19-spartan_intel-2017.u2 AmberTools consists of several independently developed packages that work well by themselves, and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models. Anaconda2: Anaconda2/4.2.0, Anaconda2/5.1.0, Anaconda2/5.3.0, Anaconda2/2018.12, Anaconda2/2019.03, Anaconda2/2019.10 Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture. Anaconda3: Anaconda3/5.0.1, Anaconda3/5.1.0, Anaconda3/5.3.0, Anaconda3/5.3.1, Anaconda3/2019.03, Anaconda3/2020.02 Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture. Armadillo: Armadillo/6.600.4-intel-2016.u3-Python-2.7.10, Armadillo/6.600.4-intel-2016.u3-Python-2.7.11, ... Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. Array-Utils: Array-Utils/0.5-intel-2016.u3 small utils for array manipulation Aspera-Connect: Aspera-Connect/3.6.1 Connect is an install-on-demand Web browser plug-in that facilitates high-speed uploads and downloads with an Aspera transfer server. Autoconf: Autoconf/2.69-foss-2017b, Autoconf/2.69-GCC-4.6.4, Autoconf/2.69-GCC-4.9.2, Autoconf/2.69-GCC-5.4.0, ... Automake: Automake/1.11-GCC-4.9.2, Automake/1.14-GCC-4.9.2, Automake/1.14-intel-2018.u4, Automake/1.14.1-foss-2017b, ... Autotools: Autotools/20150119-foss-2017b, Autotools/20150119-GCC-4.6.4, Autotools/20150119-GCC-4.9.2, Autotools/20150119-GCC-5.4.0, ... This bundle collect the standard GNU build tools: Autoconf, Automake and libtool - Homepage: http://autotools.io BAMM: BAMM/2.5.0-spartan_intel-2017.u2 BAMM is oriented entirely towards detecting and quantifying heterogeneity in evolutionary rates. It uses reversible jump Markov chain Monte Carlo to automatically explore a vast universe of candidate models of lineage diversification and trait evolution. BBMap: BBMap/36.62-intel-2016.u3-Java-1.8.0_71, BBMap/37.68, BBMap/37.93, BBMap/38.22 BBMap short read aligner, and other bioinformatic tools. - Homepage: https://sourceforge.net/projects/bbmap/ BCFtools: BCFtools/1.2-intel-2016.u3, BCFtools/1.3-intel-2016.u3, BCFtools/1.3.1-intel-2016.u3, BCFtools/1.6-intel-2017.u2, ... Samtools is a suite of programs for interacting with high-throughput sequencing data. BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants BEDTools: BEDTools/2.25.0-intel-2016.u3, BEDTools/2.26.0-intel-2016.u3, BEDTools/2.26.0-intel-2017.u2, BEDTools/2.27.1-foss-2017b, ... BLACS: BLACS/1.1-goolf-2015a, BLACS/1.1-intel-2017.u2 The BLACS (Basic Linear Algebra Communication Subprograms) project is an ongoing investigation whose purpose is to create a linear algebra oriented message passing interface that may be implemented efficiently and uniformly across a large range of distributed memory platforms. - Homepage: http://www.netlib.org/blacs/ BLAST: BLAST/2.2.26-Linux_x86_64 BLAST+: BLAST+/2.7.1-GCC-6.2.0-Python-3.5.2, BLAST+/2.7.1-intel-2016.u3, BLAST+/2.7.1-intel-2017.u2, BLAST+/2.7.1-spartan_gcc-6.2.0, ... Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. BLAT: BLAT/3.5-intel-2016.u3 BLIS: BLIS/0.5.1-GCC-6.2.0-Python-2.7.13, BLIS/0.5.1-GCC-8.2.0-Python-2.7.13 BTKCore: BTKCore/0.3.01-GCC-6.2.0 Core of the project Biomechanical-ToolKit (BTK) which represent biomechanical data, file formats and data processing BUSCO: BUSCO/4.0.0-spartan_intel-2017.u2 Based on evolutionarily-informed expectations of gene content of near-universal single-copy orthologs, BUSCO metric is complementary to technical metrics like N50. BWA: BWA/0.6.2-GCC-4.9.2, BWA/0.6.2-intel-2016.u3, BWA/0.7.10-intel-2016.u3, BWA/0.7.12-GCC-4.9.2, BWA/0.7.12-intel-2016.u3, ... BamTools: BamTools/2.3.0-intel-2016.u3, BamTools/2.4.0-intel-2016.u3, BamTools/2.4.1-intel-2017.u2, BamTools/2.5.1-foss-2017b, ... Barrnap: Barrnap/0.6-intel-2016.u3 Barrnap predicts the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S). Bazel: Bazel/0.8.0, Bazel/0.11.0-GCC-6.4.0 Bazel is a build tool that builds code quickly and reliably. It is used to build the majority of Google's software. Beast: Beast/1.8.3-intel-2016.u3, Beast/1.8.3, Beast/1.8.4-spartan_intel-2017.u2, Beast/1.10.1-spartan_intel-2017.u2, ... BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. Bicycle: Bicycle/1.8.1-intel-2018.u4-Java-9.0.4 bicycle (bisulfite-based methylcytosine caller) is a next-generation sequencing bioinformatic pipeline aimed to analyze whole genome bisulfite sequencing data. It can process data from directional (Lister) and non-directional (Cokus) bisulfite sequencing protocols, and from single-end and paired-end sequencing, and performs methylation calls for cytosines in CG and non-CG contexts (CHG and CHH). Bio-DB-HTS: Bio-DB-HTS/2.11-foss-2017b-Perl-5.26.0, Bio-DB-HTS/2.11-intel-2016.u3-Perl-5.26.2 Read files using HTSlib including BAM/CRAM, Tabix and BCF database files BioPerl: BioPerl/1.6.924-intel-2016.u3-Perl-5.20.0-bio, BioPerl/1.6.924-intel-2016.u3-Perl-5.20.0, ... Bioperl is the product of a community effort to produce Perl code which is useful in biology. Examples include Sequence objects, Alignment objects and database searching objects. Biopython: Biopython/1.61-intel-2016.u3-Python-2.7.10, Biopython/1.63-intel-2017.u2-Python-2.7.11, ... Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics. Bismark: Bismark/0.20.0-intel-2016.u3 A tool to map bisulfite converted sequence reads and determine cytosine methylation states Bison: Bison/2.7-GCC-4.9.2, Bison/2.7-intel-2016.u3, Bison/2.7, Bison/3.0.2-goolf-2015a, Bison/3.0.2-intel-2016.u3, ... Blender: Blender/2.77a-intel-2016.u3-Python-3.5.2, Blender/2.78a-intel-2016.u3-Python-3.5.2 Blender is the free and open source 3D creation suite. It supports the entirety of the 3D pipeline-modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing and game creation. - Homepage: https://www.blender.org/ Blosc: Blosc/1.12.1-intel-2017.u2 Blosc, an extremely fast, multi-threaded, meta-compressor library Boost: Boost/1.46.1-goolf-2015a, Boost/1.54.0-GCC-4.9.2-Python-2.7.9, Boost/1.54.0-intel-2016.u3-Python-2.7.9, ... Boost provides free peer-reviewed portable C++ source libraries. Boost.Python: Boost.Python/1.61.0-intel-2017.u2-GCC-6.2.0-CUDA9-Python-3.6.4, Boost.Python/1.70.0-spartan_gcc-8.1.0-Python-3.7.3 Boost.Python is a C++ library which enables seamless interoperability between C++ and the Python programming language. Bowtie: Bowtie/1.2.1.1-intel-2017.u2, Bowtie/1.2.1.1 Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end). Bowtie2: Bowtie2/2.1.0-intel-2016.u3, Bowtie2/2.2.5-GCC-4.9.2, Bowtie2/2.2.5-intel-2016.u3, Bowtie2/2.2.9-GCC-4.9.2, ... Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes. Bracken: Bracken/1.0.0, Bracken/2.2.0 Bracken: estimating species abundance in metagenomics data BreakDancer: BreakDancer/1.4.5-GCC-6.2.0, BreakDancer/1.4.5-intel-2017.u2 BreakDancer is a Perl/C++ package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads CAT: CAT/06092016-intel-2016.u3 CD-HIT: CD-HIT/4.6.1-intel-2016.u3-2012-08-27, CD-HIT/4.6.8-foss-2017b, CD-HIT/4.6.8-GCCcore-6.4.0, CD-HIT/4.6.8-intel-2017.u2, ... CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences. CESM: CESM/1.0.6 CFITSIO: CFITSIO/3.45-iccifort-2017.u2-GCC-6.2.0, CFITSIO/3.45-intel-2017.u2, CFITSIO/3.45-spartan_gcc-6.2.0 CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format. CGAL: CGAL/4.7-intel-2016.u3-Python-2.7.9, CGAL/4.7-intel-2016.u3-Python-2.7.11, CGAL/4.8.1-intel-2016.u3, CGAL/4.11-foss-2017b, ... The goal of the CGAL Open Source Project is to provide easy access to efficient and reliable geometric algorithms in the form of a C++ library. CGEPack: CGEPack/2019-goolf-2015a CGEPACK is a clone of GEMPACK - a matrix language specialised in solving CGE models. Not just a simple clone, our CGEPACK is a whole new matrix language that is more advanced than GEMPACK in many ways. CIRI: CIRI/2.0.6-intel-2018.u4-Perl-5.26.2 CircRNA Identifier. A de novo circular RNA identification tool CLCGenomicsWorkbench: CLCGenomicsWorkbench/12.0_64 CLC Genomics Workbench is used by tens of thousands of researchers all over the world for DNA, RNA, and protein sequence data analysis. Its wide variety of features are presented in an intuitive graphical user-interface, for which advanced computer skills are not required. CLCWorkbench: CLCWorkbench/8.0.1_64 CLC Main Workbench is used by tens of thousands of researchers all over the world for DNA, RNA, and protein sequence data analysis. Its wide variety of features are presented in an intuitive graphical user-interface, for which advanced computer skills are not required. CLISP: CLISP/2.49-GCC-6.2.0, CLISP/2.49-GCCcore-6.4.0 Common Lisp is a high-level, general-purpose, object-oriented, dynamic, functional programming language. CMake: CMake/2.8.4-intel-2016.u3, CMake/2.8.12-GCC-4.9.2, CMake/2.8.12-intel-2016.u3, CMake/3.0.1-intel-2016.u3, ... CNTKCustomMKL: CNTKCustomMKL/3 This is a custom version of Intel's Math Kernel Library for Microsoft's Cognitive Toolkit, packaged by the CNTK team. I have no idea why Microsoft keeps doing things like this, their ostensible reasoning is that this means users don't need access to the (now freely available) Intel MKL. Ok. --Dan - Homepage: https://github.com/Microsoft/CNTK/ COMSOL: COMSOL/5.2, COMSOL/5.3a, COMSOL/5.4 COMSOL is a cross-platform finite element analysis, solver and multipyhsics simulation software CPLEX: CPLEX/12.7.1, CPLEX/12.8, CPLEX/12.63 CPMD: CPMD/3.9-prova8, CPMD/3.15.1-QMMM_PLUMEDpatch_MN3v2, CPMD/4.3-intel-2018.u4 The CPMD code is a parallelized plane wave / pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics. CRISPR: CRISPR/1.2-Java-1.8.0_152 CRISPR Recognition Tool CUDA: CUDA/7.0.28-GCC-4.9.2, CUDA/7.0.28-intel-2016.u3, CUDA/7.0.28, CUDA/7.5.18-GCC-4.9.2, CUDA/7.5.18-intel-2016.u3, CUDA/7.5.18, ... CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs. CUSP: CUSP/0.51-CUDA9-spartan_intel-2017.u2 CUSP : A C++ Templated Sparse Matrix Library - CUDA9 custom branch CUnit: CUnit/2.1.3-intel-2017.u2 Automated testing framework for 'C'. Caffe: Caffe/1.0-intel-2017.u2-CUDA-9.1.85-Python-2.7.13, Caffe/20171110-intel-2017.u2-GCC-5.4.0-CUDA8 Caffe is a deep learning framework made with expression, speed, and modularity in mind. It is developed by the Berkeley Vision and Learning Center (BVLC) and community contributors. Caffe_unet: Caffe_unet/99bd99_20190109-intel-2017.u2-CUDA-9.1.85 Caffe is a deep learning framework made with expression, speed, and modularity in mind. It is developed by the Berkeley Vision and Learning Center (BVLC) and community contributors. Canu: Canu/1.3-GCC-4.9.3, Canu/1.7-GCC-4.9.3, Canu/1.8-GCC-6.2.0 Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION). CapnProto: CapnProto/0.6.1-GCC-6.2.0 Cap’n Proto is an insanely fast data interchange format and capability-based RPC system. Charm++: Charm++/6.6.1-intel-2016.u3 Charm++ is a message-passing parallel language and runtime system. It is implemented as a set of libraries for C++, is efficient, and is portable to a wide variety of parallel machines. Source code is provided, and non-commercial use is free. Chaste: Chaste/2017.1-intel-2016.u3 Chaste (Cancer, Heart and Soft Tissue Environment) is a general purpose simulation package aimed at multi-scale, computationally demanding problems arising in biology and physiology. Current functionality includes tissue and cell level electrophysiology, discrete tissue modelling, and soft tissue modelling. CheMPS2: CheMPS2/1.6-intel-2016.u3 Chloroplast-Genome-Assembly: Chloroplast-Genome-Assembly/13042017-intel-2017.u2 This pipeline was developed to assembly whole chloroplast genomes from genome shotgun data from Illumina. Any high-throughput sequencing data should work, but we have mostly tested with Illumina. Circos: Circos/0.69-3-intel-2016.u3-Perl-5.20.0 CisTEM: CisTEM/1.0.0-beta-intel-linux cisTEM is user-friendly software to process cryo-EM images and obtain high-resolution 3D reconstructions from them. Its name derives from âmputational imaging system for transmission electron microscopyâses a number of tools to process image data including movies, micrographs and stacks of single-particle images. Clang: Clang/7.0.0-GCC-6.2.0 C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC. ClonalFrameML: ClonalFrameML/20160309-intel-2016.u3 ClonalFrameML is a software package that performs efficient inference of recombination in bacterial genomes. ClonalFrameML was created by Xavier Didelot and Daniel Wilson. ClonalFrameML can be applied to any type of aligned sequence data, but is especially aimed at analysis of whole genome sequences. It is able to compare hundreds of whole genomes in a matter of hours on a standard Desktop computer. Cloudy: Cloudy/17.01-GCC-4.9.2 Cloudy is a spectral synthesis code designed to simulate conditions in interstellar matter under a broad range of conditions. Code_Saturne: Code_Saturne/4.0.0-intel-2016.u3 Code_Saturne solves the Navier-Stokes equations for 2D, 2D-axisymmetric and 3D flows - Homepage: http://code-saturne.org Coinhsl: Coinhsl/2014.01.10-goolf-2015a "HSL provides a number of linear solvers that can be used in IPOPT. ConnectomeWorkbench: ConnectomeWorkbench/1.3.2-intel-2017.u2 CppUnit: CppUnit/r606-GCC-4.9.2, CppUnit/1.12.1-intel-2016.u3 CppUnit is the C++ port of the famous JUnit framework for unit testing. - Homepage: http://sourceforge.net/projects/cppunit/ CrossMap: CrossMap/0.4.1-spartan_intel-2017.u2-Python-3.6.4 CrossMap is a program for genome coordinates conversion between different assemblies (such as hg18 (NCBI36) <=> hg19 (GRCh37)). It supports commonly used file formats including BAM, CRAM, SAM, Wiggle, BigWig, BED, GFF, GTF and VCF. Cube: Cube/4.2-goolf-2015a, Cube/4.3.4-goolf-2015a Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity. Cufflinks: Cufflinks/2.2.1-GCC-4.9.2, Cufflinks/2.2.1-intel-2016.u3 Cython: Cython/0.28.5-intel-2017.u2-Python-2.7.11 The Cython language makes writing C extensions for the Python language as easy as Python itself. Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations. DALTON: DALTON/2016-spartan_intel-2017.u2, DALTON/2018.1-spartan_intel-2017.u2-64bit Dalton program is designed to allow convenient, automated determination of a large number of molecular properties based on an HF, DFT, MP2, coupled cluster, or MCSCF reference wave function. DB: DB/2.7.7-GCC-4.9.2, DB/2.7.7-intel-2016.u3, DB/2.7.7-intel-2018.u4, DB/5.0.26-GCC-4.9.2, DB/6.2.32-GCC-6.2.0, ... DBD-mysql: DBD-mysql/4.048-foss-2017b-Perl-5.26.0 Perl binding for MySQL DB_File: DB_File/1.831-intel-2016.u3-Perl-5.20.0-bare, DB_File/1.831-intel-2016.u3-Perl-5.20.0-bio, ... Perl5 access to Berkeley DB version 1.x. DBus: DBus/1.10.12-goolf-2015a, DBus/1.10.12-intel-2016.u3, DBus/1.10.22-GCC-4.9.2, DBus/1.10.22-GCC-6.2.0, DBus/1.10.22-goolf-2015a, ... D-Bus is a message bus system, a simple way for applications to talk to one another. In addition to interprocess communication, D-Bus helps coordinate process lifecycle; it makes it simple and reliable to code a "single instance" application or daemon, and to launch applications and daemons on demand when their services are needed. DOLFIN: DOLFIN/2019.1.0.post0-spartan_gcc-8.1.0-Python-3.7.3 DOLFIN is the C++/Python interface of FEniCS, providing a consistent PSE (Problem Solving Environment) for ordinary and partial differential equations. DSK: DSK/2.3.3 DSK is a k-mer counter for reads or genomes. It takes as input a set of sequences in FASTA or FASTQ format and outputs a set of solid kmers. DSRC: DSRC/2.0rc-linux-64-bit DNA Sequence Reads Compression is an application designed for compression of data files containing reads from DNA sequencing in FASTQ format. The amount of such files can be huge, e.g., a few (or tens) of gigabytes, so a need for a robust data compression tool is clear. Usually universal compression programs like gzip or bzip2 are used for this purpose, but it is obvious that a specialized tool can work better. Deepbinner: Deepbinner/0.2.0-spartan_intel-2017.u2-Python-3.6.4 Deepbinner is a tool for demultiplexing barcoded Oxford Nanopore sequencing reads. It does this with a deep convolutional neural network classifier, using many of the architectural advances that have proven successful in image classification. Unlike other demultiplexers (e.g. Albacore and Porechop), Deepbinner identifies barcodes from the raw signal (a.k.a. squiggle) which gives it greater sensitivity and fewer unclassified reads. Delft3D: Delft3D/3.80.00-intel-2016.u3, Delft3D/4.04.01a-mpi-intel-2017.u2, Delft3D/4.04.01-intel-2017.u2, ... Delft3D is a world leading 3D modeling suite to investigate hydrodynamics, sediment transport and morphology and water quality for fluvial, estuarine and coastal environments. DendroPy: DendroPy/4.1.0-intel-2016.u3-Python-2.7.10, DendroPy/4.1.0-intel-2016.u3-Python-3.5.2, ... DendroPy is a Python library for phylogenetic computing. It provides classes and functions for the simulation, processing, and manipulation of phylogenetic trees and character matrices, and supports the reading and writing of phylogenetic data in a range of formats, such as NEXUS, NEWICK, NeXML, Phylip, FASTA, etc. DiscoSnp: DiscoSnp/2.5.4 DiscoSnp is designed for discovering all kinds of SNPs (not only isolated ones), as well as insertions and deletions, from raw set(s) of reads. Doxygen: Doxygen/1.8.8-GCC-4.9.2, Doxygen/1.8.8-intel-2016.u3, Doxygen/1.8.11-foss-2017b, Doxygen/1.8.11-intel-2016.u3, ... Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D. Drishti: Drishti/2.6.3-Java-1.8.0_71 Drishti is an open-source scientific visualisation software designed by Ajay Limaye at the National Computational Infrastructure's VizLab. The central idea of Drishti is that scientists can use it to explore and present volumetric datasets without extensive training. ELPA: ELPA/2016.11.001.pre-intel-2017.u2 Eigenvalue SoLvers for Petaflop-Applications . EMAN2: EMAN2/2.12-intel-2016.u3-Python-2.7.9, EMAN2/2.22-intel-2016.u3-Python-2.7.9, EMAN2/2.22-spartan_intel-2017.u2-Python-2.7.13 EMAN2 is the successor to EMAN1. It is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes. EMBOSS: EMBOSS/6.6.0-intel-2016.u3, EMBOSS/6.6.0-spartan_intel-2017.u2 EasyBuild: EasyBuild/2.4.0, EasyBuild/2.5.0, EasyBuild/2.9.0, EasyBuild/3.0.0, EasyBuild/3.0.1, EasyBuild/3.0.2, EasyBuild/3.4.1, ... EasyDict: EasyDict/1.8-intel-2016.u3-Python-3.5.2 EasyDict allows to access dict values as attributes (works recursively). A Javascript-like properties dot notation for python dicts.. Eigen: Eigen/3.2.3-GCC-4.9.2, Eigen/3.2.3-intel-2016.u3, Eigen/3.2.8-intel-2016.u3, Eigen/3.2.9-GCC-6.2.0, Eigen/3.2.9-intel-2016.u3, ... Eigensoft: Eigensoft/7.2.1-intel-2018.u4 The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification correction method (Price et al. 2006). Emacs: Emacs/25.3-GCC-4.9.2, Emacs/25.3-GCC-4.9.3 Emacs runs on several operating systems regardless of the machine type. The main ones are: GNU, GNU/Linux, FreeBSD, NetBSD, OpenBSD, macOS, MS Windows and Solaris. Env-Path: Env-Path/0.19-intel-2016.u3-Perl-5.20.0 Advanced operations on path variables Exonerate: Exonerate/2.2.0-intel-2016.u3 Exonerate is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics. FALCON: FALCON/2018.03.12-04.00-spartan_gcc-6.2.0 FALCON is a diploid aware genome assembler designed for Pacific Biosciences long read data. FASTX-Toolkit: FASTX-Toolkit/0.0.14-GCC-4.9.2 FDS: FDS/6.5.2-intel-2016.u3, FDS/6.7.0-spartan_intel-2017.u2 Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and heat transport from fires. - Homepage: https://pages.nist.gov/fds-smv/ FEniCS: FEniCS/2019.1.0.post0-spartan_gcc-8.1.0 This bundle collect the standard GNU build tools: Autoconf, Automake and libtool FFC: FFC/1.6.0-intel-2016.u3-Python-2.7.9, FFC/1.6.0-intel-2016.u3-Python-2.7.11, FFC/2016.1.0-intel-2016.u3-Python-2.7.11, ... FEniCS Form Compiler (FFC) works as a compiler for multilinear forms by generating code (C++) for the evaluation of a multilinear form given in mathematical notation. - Homepage: https://bitbucket.org/fenics-project/ffc FFTW: FFTW/2.1.5-intel-2016.u3, FFTW/3.3.4-GCC-4.9.2, FFTW/3.3.4-GCC-5.4.0, FFTW/3.3.4-GCC-6.2.0, FFTW/3.3.4-PGI-16.10-GCC-5.4.0-2.26, ... FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data. - Homepage: http://www.fftw.org FFmpeg: FFmpeg/3.1.3-GCC-4.9.2, FFmpeg/3.1.3-intel-2016.u3, FFmpeg/3.1.3-intel-2017.u2-GCC-5.4.0-CUDA8, ... A complete, cross-platform solution to record, convert and stream audio and video. FIAT: FIAT/1.5.0-goolf-2015a-Python-2.7.10, FIAT/1.5.0-intel-2016.u3-Python-2.7.9, FIAT/1.6.0-intel-2016.u3-Python-2.7.9, ... The FInite element Automatic Tabulator FIAT supports generation of arbitrary order instances of the Lagrange elements on lines, triangles, and tetrahedra. It is also capable of generating arbitrary order instances of Jacobi-type quadrature rules on the same element shapes. FLASH: FLASH/1.2.11 FLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate software tool to merge paired-end reads from next-generation sequencing experiments. FLASH is designed to merge pairs of reads when the original DNA fragments are shorter than twice the length of reads. FLTK: FLTK/1.3.3-intel-2016.u3, FLTK/1.3.3-intel-2017.u2-GCC-6.2.0-CUDA9, FLTK/1.3.3-intel-2017.u2, FLTK/1.3.3-spartan_intel-2017.u2 FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its built-in GLUT emulation. - Homepage: http://www.fltk.org FSL: FSL/5.0.8-intel-2016.u3, FSL/5.0.9-centos6_64, FSL/5.0.10-intel-2016.u3, FSL/5.0.11-intel-2017.u2-GCC-6.2.0-CUDA9, ... FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. FTGL: FTGL/2.1.3-rc5-intel-2016.u3, FTGL/2.1.3-rc5-spartan_intel-2017.u2 FTGL is a free open source library to enable developers to use arbitrary fonts in their OpenGL (www.opengl.org) applications. Fast-Plast: Fast-Plast/1.2.6-GCC-6.2.0-Perl-5.20.3 Fast-Plast: Rapid de novo assembly and finishing for whole chloroplast genomes FastANI: FastANI/1.1-spartan_intel-2017.u2 FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). FastEpistasis: FastEpistasis/2.07-intel-2016.u3 FastEpistasis, a software tool capable of computing tests of epistasis for a large number of SNP pairs, is an efficient parallel extension to the PLINK epistasis module. FastTree: FastTree/2.1.7-intel-2016.u3, FastTree/2.1.8-intel-2016.u3, FastTree/2.1.9-intel-2016.u3, FastTree/2.1.10-spartan_gcc-6.2.0, ... FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory. Fiji: Fiji/2.0-Java-1.8.0_71, Fiji/2.0-Java-11.0.2 Fiji is an image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis. File-Grep: File-Grep/0.02-intel-2016.u3-Perl-5.20.0 Find matches to a pattern in a series of files and related functions File-Slurper: File-Slurper/0.008-intel-2016.u3-Perl-5.20.0 A simple, sane and efficient module to slurp a file FileShareDir: FileShareDir/1.102-intel-2016.u3-Perl-5.20.0 The intent of File::ShareDir is to provide a companion to Class::Inspector and File::HomeDir, modules that take a process that is well-known by advanced Perl developers but gets a little tricky, and make it more available to the larger Perl community. Filtlong: Filtlong/0.2.0-spartan_gcc-6.2.0 Filtlong is a tool for filtering long reads by quality.. Flye: Flye/2.4-intel-2017.u2-Python-2.7.13 Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies. Fox: Fox/1.6.54-GCC-4.9.2 "FOX stands for Free Objects for X. It is a C++ based class library for building Graphical User Interfaces. - Homepage: http://www.fox-toolkit.org/ FragGeneScan: FragGeneScan/1.3.0-intel-2016.u3, FragGeneScan/1.3.0-intel-2017.u2, FragGeneScan/1.31-intel-2017.u2 FragGeneScan is an application for finding (fragmented) genes in short reads. It can also be applied to predict prokaryotic genes in incomplete assemblies or complete genomes. FreeSurfer: FreeSurfer/5.3.0-GCC-4.9.2-centos6_x86_64, FreeSurfer/5.3.0-intel-2016.u3-centos4_x86_64, ... FriBidi: FriBidi/1.0.1-intel-2018.u4, FriBidi/1.0.1-spartan_gcc-6.2.0 FriBidi is a free implementation of the Unicode Bidirectional (BiDi) Algorithm. It also provides utility functions to aid in the development of interactive editors and widgets that implement BiDi functionality. The BiDi algorithm is a prerequisite for supporting right-to-left scripts such as Hebrew, Arabic, Syriac, and Thaana. GAMESS-US: GAMESS-US/20160708-GCC-4.9.2 GAMS: GAMS/24.1 GATK: GATK/3.3-0-Java-1.7.0_80, GATK/3.4-46-Java-1.8.0_71, GATK/3.6-Java-1.8.0_71, GATK/3.7-Java-1.8.0_71, GATK/4.0.1.2-Java-1.8.0_71, ... The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. GCC: GCC/4.4.7, GCC/4.6.4, GCC/4.7.4, GCC/4.8.1, GCC/4.9.2-binutils-2.25, GCC/4.9.2, GCC/4.9.3, GCC/4.9.3-2.25, GCC/4.9.4, GCC/5.2.0, ... GCC-CUDA: GCC-CUDA/5.4.0-8.0.61, GCC-CUDA/6.2.0-9.0.176 The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...). This version also GCCcore: GCCcore/4.9.3, GCCcore/5.4.0, GCCcore/6.3.0, GCCcore/6.4.0, GCCcore/7.3.0, GCCcore/8.1.0, GCCcore/8.2.0, GCCcore/8.3.0 The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...). GConf: GConf/3.2.6-GCC-6.2.0, GConf/3.2.6-intel-2017.u2 GConf is a system for storing application preferences. It is intended for user preferences; not configuration of something like Apache, or arbitrary data storage. GD: GD/2.52-intel-2016.u3-Perl-5.20.0, GD/2.56-intel-2016.u3-Perl-5.20.0 GDAL: GDAL/1.10.0-GCC-4.9.2, GDAL/1.10.0-intel-2016.u3, GDAL/2.0.0-GCC-4.9.2, GDAL/2.0.0-intel-2016.u3, GDAL/2.1.3-GCC-4.9.2, ... GDB: GDB/7.8.2-GCC-4.9.2, GDB/7.8.2-goolf-2015a GEMINI: GEMINI/0.18.3-GCC-4.9.2-Python-2.7.9 GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. GEOS: GEOS/3.6.1-intel-2016.u3-Python-2.7.11, GEOS/3.6.1-intel-2016.u3-Python-2.7.12, GEOS/3.6.2-spartan_gcc-6.2.0-Python-3.7.3, ... GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS) GHC: GHC/6.12.3-GCC-4.9.2, GHC/6.12.3-intel-2016.u3 The Glorious/Glasgow Haskell Compiler GL2PS: GL2PS/1.4.0-intel-2017.u2, GL2PS/1.4.0-spartan_gcc-6.2.0 GL2PS: an OpenGL to PostScript printing library GLINT: GLINT/1.0.4-Python.2.7.13-intel-2017.u2 GLINT is a user-friendly command-line tool for fast analysis of genome-wide DNA methylation data generated using the Illumina human methylation arrays. GLINT allows to easily run a pipeline of Epigenome-Wide Association Study (EWAS) under different models while accounting for known confounders in methylation data. GLM: GLM/0.9.7.2-intel-2016.u3, GLM/0.9.7.2-intel-2017.u2, GLM/0.9.9.0-spartan_gcc-8.1.0 OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics software based on the OpenGL Shading Language (GLSL) specifications. - Homepage: https://github.com/g-truc/glm GLee: GLee/5.4-intel-2017.u2-GCC-6.2.0-CUDA9 GLib: GLib/2.40.0-intel-2016.u3, GLib/2.46.0-intel-2016.u3-Python-2.7.9, GLib/2.46.0-intel-2016.u3-Python-2.7.11, ... GMAP-GSNAP: GMAP-GSNAP/2014-06-10-GCC-4.9.2 GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences GSNAP: Genomic Short-read Nucleotide Alignment Program GMP: GMP/5.1.3-GCC-4.9.2, GMP/6.0.0a-GCC-4.9.2, GMP/6.0.0a-GCC-4.9.3, GMP/6.0.0a-iomkl-2016.u3, GMP/6.0.0a-iompi-2016.u3, ... GMSH: GMSH/2.16.0-intel-2016.u3 Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor. - Homepage: http://geuz.org/gmsh GNU: GNU/4.9.2-2.25 Compiler-only toolchain with GCC and binutils. - Homepage: http://www.gnu.org/software/ GObject-Introspection: GObject-Introspection/1.47.1-GCC-4.9.2, GObject-Introspection/1.47.1-goolf-2015a, ... GObject introspection is a middleware layer between C libraries (using GObject) and language bindings. The C library can be scanned at compile time and generate a metadata file, in addition to the actual native C library. Then at runtime, language bindings can read this metadata and automatically provide bindings to call into the C library. - Homepage: https://wiki.gnome.org/GObjectIntrospection/ GROMACS: GROMACS/4.6.5-intel-2016.u3-mpi, GROMACS/4.6.5-intel-2016.u3-mt, GROMACS/4.6.7-spartan_intel-2017.u2-mpi, ... GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. GSL: GSL/1.16-intel-2016.u3, GSL/1.16-spartan_intel-2017.u2, GSL/2.1-GCC-4.9.2, GSL/2.1-goolfc-2017.01, GSL/2.1-intel-2016.u3, ... GST-plugins-base: GST-plugins-base/0.10.36-GCC-6.2.0, GST-plugins-base/0.10.36-intel-2017.u2 GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio (mixing) and video (non-linear editing) processing. GStreamer: GStreamer/0.10.36-GCC-6.2.0, GStreamer/0.10.36-intel-2017.u2, GStreamer/1.10.3-GCC-6.2.0, GStreamer/1.10.3-intel-2016.u3, ... GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio (mixing) and video (non-linear editing) processing. GTK+: GTK+/2.24.28-intel-2016.u3, GTK+/2.24.31-GCC-4.9.2, GTK+/2.24.31-GCC-6.2.0, GTK+/2.24.31-intel-2016.u3, ... The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications. - Homepage: https://developer.gnome.org/gtk+/stable/ GTS: GTS/0.7.6-intel-2018.u4 GTS stands for the GNU Triangulated Surface Library. It is an Open Source Free Software Library intended to provide a set of useful functions to deal with 3D surfaces meshed with interconnected triangles. Gaussian: Gaussian/g09.b01, Gaussian/g09TEST, Gaussian/g09, Gaussian/g16c, Gaussian/g16 Gdk-Pixbuf: Gdk-Pixbuf/2.32.3-intel-2016.u3, Gdk-Pixbuf/2.36.6-GCC-4.9.2, Gdk-Pixbuf/2.36.6-GCC-6.2.0, ... The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it was distributed as part of GTK+ 2 but it was split off into a separate package in preparation for the change to GTK+ 3. - Homepage: https://developer.gnome.org/gdk-pixbuf/stable/ Gensim: Gensim/3.7.1-intel-2016.u3-Python-2.7.12, Gensim/3.7.1-intel-2017.u2-Python-2.7.13 Scalable statistical semantics, Analyze plain-text documents for semantic structure, Retrieve semantically similar documents Ghostscript: Ghostscript/9.20-intel-2016.u3, Ghostscript/9.22-intel-2018.u4-cairo-1.14.8 Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to different targets. It used to be part of the cups printing stack, but is no longer used for that. Go: Go/1.5.1, Go/1.8.1, Go/1.11.5, Go/1.14.1 Go is an open source programming language that makes it easy to build simple, reliable, and efficient software. GrADS: GrADS/2.2.0-GCC-4.9.2 The Grid Analysis and Display System (GrADS) is an interactive desktop tool that is used for easy access, manipulation, and visualization of earth science data. Graph: Graph/0.9704-intel-2016.u3-Perl-5.20.0 graph data structures and algorithms Graphviz: Graphviz/2.40.1-intel-2018.u4 Graphviz is open source graph visualization software. Graph visualization is a way of representing structural information as diagrams of abstract graphs and networks. It has important applications in networking, bioinformatics, software engineering, database and web design, machine learning, and in visual interfaces for other technical domains. Greenlet: Greenlet/0.4.9-intel-2016.u3-Python-3.5.2 The greenlet package is a spin-off of Stackless, a version of CPython that supports micro-threads called "tasklets". Tasklets run pseudo-concurrently (typically in a single or a few OS-level threads) and are synchronized with data exchanges on "channels". A "greenlet", on the other hand, is a still more primitive notion of micro-thread with no implicit scheduling; coroutines, in other words. This is useful when you want to control exactly when your code runs. Gubbins: Gubbins/1.4.2-intel-2016.u3-Python-2.7.9, Gubbins/2.3.4-intel-2016.u3-Python-3.5.2 Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. - Homepage: https://github.com/andrewjpage/gubbins Guidance2: Guidance2/2.02-intel-2017.u2 The GUIDANCE web-server is a powerful and user-friendly tool for assigning a confidence score for each residue, column, and sequence in an alignment and for projecting these scores onto the MSA [1]. The server points to columns and sequences that are unreliably aligned and enables their automatic removal from the MSA, in preparation for downstream analyses. Guile: Guile/1.8.8-spartan_gcc-6.2.0 Guile is the GNU Ubiquitous Intelligent Language for Extensions, the official extension language for the GNU operating system. Guppy: Guppy/2.3.1-cpu, Guppy/2.3.1-rpm, Guppy/3.2.4 Guppy software supports MinIT and MinION instruments from Nanopore Technologies Gurobi: Gurobi/7.0.1, Gurobi/8.1.1, Gurobi/9.0.0 The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern architectures and multi-core processors, using the most advanced implementations of the latest algorithms. - Homepage: http://www.gurobi.com HDDM: HDDM/0.7.1-intel-2017.u2-Python-3.6.1 HDDM is a Puthon toolbox for hierarchical Bayesian parameter estimation of the Drift Diffusion Model (via PyMC). HDF: HDF/4.2.8-GCC-4.9.2, HDF/4.2.8-intel-2016.u3, HDF/4.2.8-intel-2017.u2 HDF5: HDF5/1.8.12-intel-2016.u3, HDF5/1.8.13-GCC-4.9.2, HDF5/1.8.13-intel-2016.u3, HDF5/1.8.15-patch1-intel-2016.u3, ... HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections. - Homepage: http://www.hdfgroup.org/HDF5/ HGA: HGA/1.0.0-Python-2.7.10 Hierarchical Genome Assembly (HGA) is a novel methodology that takes further advantage of very high coverage by independently assembling disjoint subsets of reads, combining assemblies of the subsets, and finally re-assembling the combined contigs along with the original reads. HGA_pymodules-bundle: HGA_pymodules-bundle/1.0.0-intel-2016.u3-Python-2.7.10 This is a bundle of two python modules, xlrd and xlwt, required by the application, HGA (separate module). xlrd (https://pypi.python .org/pypi/xlrd) extracts data from Microsoft Excel spreadsheets, while xlwt (https://pypi.python.org/pypi/xlwt) is used to generate Excel spreadsheet s. HISAT2: HISAT2/2.1.0-intel-2016.u3 HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). - Homepage: https://ccb.jhu.edu/software/hisat2/index.shtml HMMER: HMMER/3.1b2-intel-2016.u3, HMMER/3.1b2-intel-2017.u2, HMMER/3.2.1-foss-2017b, HMMER/3.2.1-intel-2017.u2, ... HPL: HPL/2.1-intel-2016.u3 HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the High Performance Computing Linpack Benchmark. HTSeq: HTSeq/0.9.1-GCC-6.2.0-Python-2.7.13, HTSeq/0.9.1-intel-2016.u3-Python-2.7.12, HTSeq/0.9.1-intel-2017.u2-Python-2.7.13 HTSlib: HTSlib/1.2.1-intel-2016.u3, HTSlib/1.3-intel-2016.u3, HTSlib/1.3.1-intel-2016.u3, HTSlib/1.4.1-intel-2016.u3, ... A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix HarfBuzz: HarfBuzz/1.1.3-GCC-4.9.2, HarfBuzz/1.1.3-goolf-2015a, HarfBuzz/1.1.3-intel-2016.u3, HarfBuzz/1.4.6-foss-2017b, ... HarfBuzz is an OpenType text shaping engine. - Homepage: http://www.freedesktop.org/wiki/Software/HarfBuzz Horovod: Horovod/0.19.0-intel-2017.u2-GCC-6.2.0-CUDA9-TensorFlow-2.1.0-Python-3.6.4 Horovod is a distributed training framework for TensorFlow. HyPhy: HyPhy/2.3.14-spartan_intel-2017.u2 HyPhy is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. Hypre: Hypre/2.11.1-goolf-2015a, Hypre/2.11.1-intel-2016.u3-test, Hypre/2.11.1-intel-2016.u3, Hypre/2.15.1-spartan_gcc-8.1.0 Hypre is a library for solving large, sparse linear systems of equations on massively parallel computers. The problems of interest arise in the simulation codes being developed at LLNL and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences. I-TASSER: I-TASSER/4.2, I-TASSER/5.0 I-TASSER (Iterative Threading ASSEmbly Refinement) is a hierarchical method for protein structure and function prediction. Structural templates are identified from the PDB by multiple threading approach LOMETS; full-length atomic models are then constructed by iterative template fragment assembly simulations; function inslights of the target are finally derived by threading the 3D models through protein function database BioLiP. ICU: ICU/60.2-GCC-4.9.2, ICU/61.1-GCC-6.2.0, ICU/61.1-intel-2017.u2, ICU/61.1-intel-2018.u4, ICU/61.1-spartan_gcc-6.2.0, ... ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications. ICU is widely portable and gives applications the same results on all platforms and between C/C++ and Java software. . IDBA: IDBA/1.1.3-GCC-4.9.3, IDBA/1.1.3-intel-2017.u2 IDBA is the basic iterative de Bruijn graph assembler for second-generation sequencing reads. IDBA-UD, an extension of IDBA, is designed to utilize paired-end reads to assemble low-depth regions and use progressive depth on contigs to reduce errors in high-depth regions. IGV: IGV/2.3.15 The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations. IOR: IOR/3.0.1-gompi-2015a-mpiio The IOR software is used for benchmarking parallel file systems using POSIX, MPIIO, or HDF5 interfaces. - Homepage: https://github.com/chaos/ior IPC-System-Simple: IPC-System-Simple/1.25-intel-2016.u3-Perl-5.20.0 IPC::System::Simple - Run commands simply, with detailed diagnostics. IPython: IPython/3.2.0-intel-2016.u3-Python-2.7.9, IPython/3.2.0-spartan_intel-2017.u2-Python-2.7.13 IPython provides a rich architecture for interactive computing with: Powerful interactive shells (terminal and Qt-based). A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. Support for interactive data visualization and use of GUI toolkits. Flexible, embeddable interpreters to load into your own projects. Easy to use, high performance tools for parallel computing. - Homepage: http://ipython.org/index.html IQ-TREE: IQ-TREE/1.6.7-spartan_intel-2017.u2 Efficient phylogenomic software by maximum likelihood IRFinder: IRFinder/1.2.5-intel-2017.u2 Detecting intron retention from RNA-Seq experiments ISL: ISL/0.15-GCC-4.9.2 ITK: ITK/4.12.2-intel-2016.u3-Python-2.7.11, ITK/4.13.2-spartan_gcc-6.2.0-Python-2.7.13 Insight Segmentation and Registration Toolkit (ITK) provides an extensive suite of software tools for registering and segmenting multidimensional imaging data. ImageJ: ImageJ/152-Java-1.8.0_71 ImageJ is a Java based, platform independent image manipulation library ImageMagick: ImageMagick/7.0.2-9-GCC-4.9.2, ImageMagick/7.0.2-9-GCC-6.2.0 Infernal: Infernal/1.1.2-intel-2016.u3 Instant: Instant/1.6.0-intel-2016.u3-Python-2.7.9, Instant/1.6.0-intel-2016.u3-Python-2.7.11, ... Instant is a Python module that allows for instant inlining of C and C++ code in Python. It is a small Python module built on top of SWIG and Distutils. - Homepage: https://bitbucket.org/fenics-project/instant IntelPython: IntelPython/2.7.16-2019.5.098, IntelPython/3.6.9-2019.5.098 Intel® Distribution for Python. Powered by Anaconda. Accelerating Python* performance on modern architectures from Intel. InterViews: InterViews/19-intel-2016.u3, InterViews/19-intel-2017.u2 InterViews is a prerequisite of the NEURON, a simulation environment for building and using computational models of neurons and networks of neurons. JAGS: JAGS/4.2.0-intel-2016.u3, JAGS/4.3.0-GCC-6.2.0, JAGS/4.3.0-intel-2016.u3, JAGS/4.3.0-intel-2017.u2, ... JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation - Homepage: http://mcmc-jags.sourceforge.net/ JUnit: JUnit/4.12-Java-1.8.0_71, JUnit/4.12-Java-1.8.0_152, JUnit/4.12-Java-9.0.4 A programmer-oriented testing framework for Java. JasPer: JasPer/1.900.1-GCC-4.9.2, JasPer/1.900.1-intel-2016.u3, JasPer/1.900.1-intel-2017.u2-GCC-5.4.0-CUDA8, ... Java: Java/1.7.0_80, Java/1.8.0_71, Java/1.8.0_152, Java/9.0.4, Java/11.0.2 Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers. Jellyfish: Jellyfish/1.1.11-GCC-4.9.2, Jellyfish/2.2.6-GCC-6.2.0, Jellyfish/2.2.6-spartan_gcc-6.2.0, ... Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. Json-Fortran: Json-Fortran/6.3.0-GCC-6.2.0, Json-Fortran/6.3.0-intel-2017.u2 A user-friendly, thread-safe, and object-oriented API for reading and writing JSON files, written in modern Fortran. Julia: Julia/0.5.0-binary, Julia/0.6.0-binary, Julia/1.0.0-spartan_gcc-6.2.0, Julia/1.0.2-spartan_gcc-6.2.0, ... KNIFE: KNIFE/1.4 Known and Novel IsoForm Explorer. Statistically based splicing detection for circular and linear isoforms from RNA-Seq data. Kaiju: Kaiju/1.6.2-intel-2017.u2 Kaiju is a program for sensitive taxonomic classification of high-throughput sequencing reads from metagenomic whole genome sequencing experiments Kent_tools: Kent_tools/20181018-linux.x86_64 Kent tools: collection of tools used by the UCSC genome browser. Keras: Keras/2.1.5-intel-2017.u2-GCC-5.4.0-CUDA8-Python-3.5.2-GPU, Keras/2.1.5-intel-2017.u2-GCC-6.2.0-CUDA9-Python-3.5.2-GPU, ... Keras is a high-level neural networks API, written in Python and capable of running on top of TensorFlow, CNTK, or Theano. Kraken: Kraken/1.0-GCC-4.9.2, Kraken/1.0-intel-2017.u2-Perl-5.24.1, Kraken/1.0-spartan_gcc-6.2.0-Perl-5.26.0, ... Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Kraken2: Kraken2/2.0.6-beta-intel-2016.u3-Perl-5.26.2, Kraken2/2.0.6-beta-spartan_intel-2017.u2-Perl-5.26.0 Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. Kraken aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm. Krona: Krona/2.7 Krona allows hierarchical data to be explored with zooming, multi-layered pie charts. KyotoCabinet: KyotoCabinet/1.2.76-intel-2016.u3, KyotoCabinet/1.2.76-intel-2017.u2 Kyoto Cabinet is a library of routines for managing a database. LAMMPS: LAMMPS/patch_29Mar2019-spartan_gcc-6.2.0-cuda9.2, LAMMPS/12Dec2018-patch_28Feb-spartan_gcc-6.2.0-cuda9.2, ... LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a classical molecular dynamics simulation code designed to run efficiently on parallel computers. LANDIS-II: LANDIS-II/7.0-GCC-6.2.0 The LANDIS-II forest landscape model simulates future forests (both trees and shrubs) at decadal to multi-century time scales and spatial scales spanning hundreds to millions of hectares. LAPACK: LAPACK/3.4.2-GCC-6.2.0, LAPACK/3.4.2-intel-2017.u2-GCC-6.2.0-CUDA9, LAPACK/3.5.0-GCC-4.9.2-OpenBLAS-0.2.20, ... LAPACK is written in Fortran90 and provides routines for solving systems of simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue problems, and singular value problems. LLVM: LLVM/3.7.0-GCC-4.9.2, LLVM/3.7.0-goolf-2015a, LLVM/3.7.0-intel-2016.u3, LLVM/3.7.0-intel-2017.u2, LLVM/3.7.0-iomkl-2016.u3, ... The LLVM Core libraries provide a modern source- and target-independent optimizer, along with code generation support for many popular CPUs (as well as some less common ones!) These libraries are built around a well specified code representation known as the LLVM intermediate representation ("LLVM IR"). The LLVM Core libraries are well documented, and it is particularly easy to invent your own language (or port an existing compiler) to use LLVM as an optimizer and code generator. - Homepage: http://llvm.org/ LMDB: LMDB/0.9.18-GCC-4.9.2, LMDB/0.9.18-intel-2016.u3, LMDB/0.9.18-intel-2017.u2-GCC-5.4.0-CUDA8, LMDB/0.9.21-GCC-6.2.0, ... OpenLDAP's Lightning Memory-Mapped Database (LMDB) library. - Homepage: https://github.com/LMDB/lmdb LR_Gapcloser: LR_Gapcloser/20180904 LR_Gapcloser is a gap closing tool using long reads from studied species. LZO: LZO/2.10-intel-2017.u2 Portable lossless data compression library LevelDB: LevelDB/1.18-intel-2017.u2 LevelDB is a fast key-value storage library written at Google that provides an ordered mapping from string keys to string values. LibTIFF: LibTIFF/4.0.4-goolf-2015a, LibTIFF/4.0.4-intel-2016.u3, LibTIFF/4.0.6-GCC-4.9.2, LibTIFF/4.0.6-GCC-6.2.0, ... tiff: Library and tools for reading and writing TIFF data files LibUUID: LibUUID/1.0.3-intel-2016.u3, LibUUID/1.0.3-intel-2017.u2 Portable uuid C library LightGBM: LightGBM/2.1.0-GCC-4.9.2 A fast, distributed, high performance gradient boosting (GBDT, GBRT, GBM or MART) framework based on decision tree algorithms. Lighter: Lighter/1.1.2-spartan_intel-2017.u2 Lighter is a kmer-based error correction method for whole genome sequencing data. LittleCMS: LittleCMS/2.7-goolf-2015a, LittleCMS/2.7-intel-2017.u2-GCC-5.4.0-CUDA8, LittleCMS/2.7-intel-2017.u2-GCC-6.2.0-CUDA9, ... Little CMS intends to be an OPEN SOURCE small-footprint color management engine, with special focus on accuracy and performance. Lua: Lua/5.1.4-8-GCC-4.9.2, Lua/5.1.4-8-intel-2016.u3, Lua/5.1.4-8-intel-2017.u2-GCC-5.4.0-CUDA8 Lua is a powerful, fast, lightweight, embeddable scripting language. Lua combines simple procedural syntax with powerful data description constructs based on associative arrays and extensible semantics. Lua is dynamically typed, runs by interpreting bytecode for a register-based virtual machine, and has automatic memory management with incremental garbage collection, making it ideal for configuration, scripting, and rapid prototyping. - Homepage: http://www.lua.org/ M4: M4/1.4.17-foss-2017b, M4/1.4.17-GCC-4.6.4, M4/1.4.17-GCC-4.9.2-binutils-2.25, M4/1.4.17-GCC-4.9.2, M4/1.4.17-GCC-4.9.3-2.25, ... MACS: MACS/2.1.2.1-intel-2017.u2-Python-2.7.13 MACS -- Model-based Analysis of ChIP-Seq https://github.com/taoliu/MACS MAFFT: MAFFT/7.130-GCC-4.9.2-with-extensions, MAFFT/7.130-intel-2016.u3-with-extensions, MAFFT/7.221-intel-2016.u3-with-extensions, ... MATIO: MATIO/1.5.2-intel-2016.u3, MATIO/1.5.2-intel-2017.u2, MATIO/1.5.12-spartan_gcc-8.1.0 matio is an C library for reading and writing Matlab MAT files. MATLAB: MATLAB/2016a, MATLAB/2017a, MATLAB/2018a, MATLAB/2018b, MATLAB/2019a MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran. MCL: MCL/14.137-intel-2016.u3, MCL/14.137-spartan_gcc-6.2.0, MCL/14.137-spartan_intel-2017.u2 MCR: MCR/R2016a The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed. MEGA: MEGA/10.0.5 MEGA-CC (Molecular Evolutionary Genetics Analysis Computational Core) is an integrated suite of tools for statistics-based comparative analysis of molecular sequence data based on evolutionary principles. MEGAHIT: MEGAHIT/1.0.3-intel-2016.u3, MEGAHIT/1.1.1-intel-2016.u3, MEGAHIT/1.1.1-intel-2017.u2, MEGAHIT/1.1.4-spartan_intel-2017.u2 MEGAHIT is a NGS de novo assembler for assembling large and complex metagenomics data in a time- and cost-efficient manner. MEME: MEME/5.0.5-intel-2018.u4-Perl-5.26.2-Python-3.6.4 The MEME Suite allows you to: * discover motifs using MEME, DREME (DNA only) or GLAM2 on groups of related DNA or protein sequences, * search sequence databases with motifs using MAST, FIMO, MCAST or GLAM2SCAN, * compare a motif to all motifs in a database of motifs, * associate motifs with Gene Ontology terms via their putative target genes, and * analyse motif enrichment using SpaMo or CentriMo. METIS: METIS/3.0.6-intel-2017.u2, METIS/4.0.3-intel-2016.u3, METIS/4.0.3-intel-2017.u2, METIS/5.1.0-GCC-4.9.2, METIS/5.1.0-GCC-6.2.0, ... METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes. - Homepage: http://glaros.dtc.umn.edu/gkhome/metis/metis/overview MIGRATE-N: MIGRATE-N/3.6.11-intel-2017.u2, MIGRATE-N/4.2.14-foss-2017b Migrate estimates effective population sizes and past migration rates between n population assuming a migration matrix model with asymmetric migration tates and different subpopulation sizes. MPC: MPC/1.0.2-GCC-4.9.2, MPC/1.0.2-intel-2016.u3 MPFR: MPFR/3.1.2-GCC-4.9.2, MPFR/3.1.2-intel-2016.u3, MPFR/3.1.3-GCC-4.9.2, MPFR/3.1.3-GCC-6.2.0, MPFR/3.1.3-iomkl-2016.u3, ... MPICH: MPICH/3.2.1-GCC-4.9.2, MPICH/3.2.1-GCC-6.2.0, MPICH/3.2.1-intel-2017.u2 MPICH v3.x is an open source high-performance MPI 3.0 implementation. It does not support InfiniBand (use MVAPICH2 with InfiniBand devices). MPJ-Express: MPJ-Express/0.44-goolf-2015a-Java-9.0.4 MPJ Express is an open source Java message passing library that allows application developers to write and execute parallel applications for multicore processors and compute clusters/clouds. MRtrix: MRtrix/0.3.14-intel-2016.u3-Python-2.7.9, MRtrix/0.3.14-intel-2016.u3-Python-2.7.11, MRtrix/3.0_RC2-GCC-6.2.0, ... MRtrix provides a set of tools to perform diffusion-weighted MR white-matter tractography in a manner robust to crossing fibres, using constrained spherical deconvolution (CSD) and probabilistic streamlines. - Homepage: http://www.brain.org.au/software/index.html#mrtrix MS-CG: MS-CG/1.7.3.1-intel-2017.u2-GCC-6.2.0-CUDA9.1 The Multiscale Coarse-Graining (MS-CG) method is a variational force-matching technique developed by the Voth group. This project serves as the workhorse implementation of the method used as a standard force-matching code. MTL4: MTL4/4.0.9555 The Matrix Template Library 4 incorporates the most modern programming techniques to provide an easy and intuitive interface to users while enabling optimal performance. The natural mathematical notation in MTL4 empowers all engineers and scientists to implement their algorithms and models in minimal time. All technical aspects are encapsulated in the library. - Homepage: http://www.simunova.com/mtl4 MUMPS: MUMPS/4.10.0-goolf-2015a-parmetis, MUMPS/4.10.0-intel-2017.u2-parmetis, MUMPS/5.0.1-intel-2017.u2-parmetis A parallel sparse direct solver - Homepage: http://graal.ens-lyon.fr/MUMPS/ MUMmer: MUMmer/3.23-intel-2016.u3, MUMmer/4.0.0beta2-spartan_gcc-6.2.0 MUSCLE: MUSCLE/3.8.31-intel-2016.u3, MUSCLE/3.8.31-intel-2017.u2 MVAPICH2: MVAPICH2/2.1-GCC-4.9.2, MVAPICH2/2.2b-GCC-4.9.3-2.25, MVAPICH2/2.3.2-GCC-6.2.0 This is an MPI 3.0 implementation. It is based on MPICH2 and MVICH. Mako: Mako/1.0.4-foss-2017b-Python-2.7.14, Mako/1.0.4-GCC-6.2.0-Python-2.7.13-bare, Mako/1.0.4-intel-2016.u3-Python-2.7.9, ... A super-fast templating language that borrows the best ideas from the existing templating languages Maple: Maple/2015 MariaDB: MariaDB/10.2.11-foss-2017b MariaDB An enhanced, drop-in replacement for MySQL. MariaDB-connector-c: MariaDB-connector-c/2.3.5-GCC-6.2.0, MariaDB-connector-c/2.3.5-intel-2017.u2, ... MariaDB Connector/C is used to connect applications developed in C/C++ to MariaDB and MySQL databases. Mash: Mash/2.1-intel-2017.u2, Mash/2.1-spartan_intel-2017.u2 Fast genome and metagenome distance estimation using MinHash Mathematica: Mathematica/11.0.1, Mathematica/12.0.0 Mathematica is a computational software program used in many scientific, engineering, mathematical and computing fields. - Homepage: http://www.wolfram.com/mathematica Maven: Maven/3.5.4 Binary maven install, Apache Maven is a software project management and comprehension tool. Based on the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a central piece of information. Mawk: Mawk/1.3.4-intel-2017.u2 mawk is an interpreter for the AWK Programming Language. MaxBin: MaxBin/2.2.5-intel-2017.u2 MaxBin is a software that is capable of clustering metagenomic contigs into different bins, each consists of contigs from one species. MaxBin uses the nucleotide composition information and contig abundance information to do achieve binning through an Expectation-Maximization algorithm. Maxima: Maxima/5.41.0-GCC-6.2.0, Maxima/5.41.0-GCCcore-6.4.0 Maxima is a system for the manipulation of symbolic and numerical expressions. Mesa: Mesa/7.11.2-GCC-4.9.2-Python-2.7.9, Mesa/11.0.2-GCC-4.9.2-Python-2.7.9, Mesa/11.0.2-goolf-2015a-Python-2.7.10, ... Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics. - Homepage: http://www.mesa3d.org/ Meson: Meson/0.43.0-intel-2016.u3-Python-3.5.2, Meson/0.43.0-intel-2017.u2-Python-3.5.2, Meson/0.43.0-intel-2017.u2-Python-3.6.4, ... Meson is a cross-platform build system designed to be both as fast and as user friendly as possible. Mesquite: Mesquite/2.3.0-spartan_gcc-6.2.0, Mesquite/2.3.0-spartan_intel-2017.u2 Mesh-Quality Improvement Library MetaBAT: MetaBAT/2.12.1-intel-2017.u2 Benchmark of Automated Metagenome Binning Software in Complex Metagenomes. MetaVelvet: MetaVelvet/1.2.01-intel-2016.u3, MetaVelvet/1.2.02-intel-2016.u3, MetaVelvet/1.2.02-spartan_intel-2017.u2 MindTheGap: MindTheGap/2.2.2 MindTheGap performs detection and assembly of DNA insertion variants in NGS read datasets with respect to a reference genome Miniasm: Miniasm/0.3-GCC-6.2.0 Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Miniconda2: Miniconda2/4.3.21 Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture. Miniconda3: Miniconda3/4.4.10, Miniconda3/4.5.4, Miniconda3/4.6.14 Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture. Minimac3: Minimac3/1.0.10-intel-2016.u3, Minimac3/2.0.1-intel-2016.u3 Minimac3 is a lower memory and more computationally efficient implementation of the genotype imputation algorithms in minimac and minimac2. Minimac3 is designed to handle very large reference panels in a more computationally efficient way with no loss of accuracy. - Homepage: http://genome.sph.umich.edu/wiki/Minimac3 Minimap2: Minimap2/2.13-foss-2017b, Minimap2/2.13-intel-2017.u2, Minimap2/2.15-GCC-6.2.0 Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database. Molden: Molden/5.7-GCC-4.9.2, Molden/5.7-intel-2016.u3 Molden is a package for displaying Molecular Density from the Ab Initio packages GAMESS-UK, GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac - Homepage: http://www.cmbi.ru.nl/molden/ Mono: Mono/4.6.2.7-GCC-4.9.2, Mono/4.6.2.7-intel-2016.u3, Mono/4.8.0.495-intel-2017.u2 An open source, cross-platform, implementation of C# and the CLR that is binary compatible with Microsoft.NET. - Homepage: http://mono-framework.com MotionCor2: MotionCor2/01-30-2017 Correction of electron beam-induced sample motion is one of the major factors contributing to the recent resolution breakthroughs in cryo-electron microscopy. - Homepage: http://msg.ucsf.edu/em/software/motioncor2.html MrBayes: MrBayes/3.2.6-intel-2016.u3 MrBayes is a program for the Bayesian estimation of phylogeny. MultiQC: MultiQC/1.6-intel-2017.u2-Python-3.6.4 Aggregate results from bioinformatics analyses across many samples into a single report. MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. Multiwell: Multiwell/2016-intel-2016.u3, Multiwell/2020-intel-2017.u2 Calculates time dependent concentrations, reaction yields, vibrational distributions, and rate constants as functions of temperature and pressure for multi-well, multi-channel unimolecular reactions systems. - Homepage: http://clasp-research.engin.umich.edu/multiwell/ NAMD: NAMD/2.10-gompi-2015a-mpi, NAMD/2.10-intel-2016.u3-mpi, NAMD/2.10-intel-2017.u2, NAMD/2.10-iomkl-2016.u3-mpi, ... NASM: NASM/2.11.06-intel-2016.u3, NASM/2.11.08-foss-2017b, NASM/2.11.08-GCC-4.9.2, NASM/2.11.08-GCC-6.2.0, NASM/2.11.08-goolf-2015a, ... NASM: General-purpose x86 assembler NBO: NBO/7.0-intel-2017.u2 The Natural Bond Orbital (NBO) program is a discovery tool for chemical insights from complex wavefunctions. NCBI-GENOME: NCBI-GENOME/0.2.2-intel-2016.u3-Python-2.7.10 Some script to download bacterial and fungal genomes from NCBI after they restructured their FTP a while ago. NCBI-Toolkit: NCBI-Toolkit/21.0.0-intel-2017.u2 The NCBI Toolkit is a collection of utilities developed for the production and distribution of GenBank, Entrez, BLAST, and related services by the National Center for Biotechnology Information. NCCL: NCCL/2.5.6-intel-2017.u2-GCC-6.2.0-CUDA9 The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective communication primitives that are performance optimized for NVIDIA GPUs. NCL: NCL/6.5.0 NCAR Command Language NCO: NCO/4.7.1-intel-2016.u3, NCO/4.7.1-intel-2017.u2 manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5 NEURON: NEURON/7.4-gompi-2015a, NEURON/7.4-intel-2016.u3, NEURON/7.6.2-intel-2017.u2 Empirically-based simulations of neurons and networks of neurons. - Homepage: http://www.neuron.yale.edu/neuron NEdit: NEdit/5.5-Linux-x86 NEdit is a multi-purpose text editor for the X Window System, which combines a standard, easy to use, graphical user interface with the thorough functionality and stability required by users who edit text eight hours a day. NGS: NGS/2.9.3-spartan_intel-2017.u2-Java-1.8.0_152 NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. NLopt: NLopt/2.4.2-GCC-6.2.0, NLopt/2.4.2-intel-2017.u2, NLopt/2.4.2-intel-2018.u4, NLopt/2.4.2-spartan_intel-2017.u2, ... NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms. NSPR: NSPR/4.9.3-GCC-6.2.0, NSPR/4.21-intel-2017.u2, NSPR/4.21-spartan_gcc-6.2.0, NSPR/4.21-spartan_gcc-8.1.0, ... Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level and libc-like functions. NSS: NSS/3.42.1-intel-2017.u2, NSS/3.42.1-spartan_gcc-6.2.0, NSS/3.42.1-spartan_gcc-8.1.0 Network Security Services (NSS) is a set of libraries designed to support cross-platform development of security-enabled client and server applications. NWChem: NWChem/6.5.revision26243-intel-2016.u3-2014-09-10-Python-2.7.11 NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. NWChem software can handle: biomolecules, nanostructures, and solid-state; from quantum to classical, and all combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of processors; properties and relativity. - Homepage: http://www.nwchem-sw.org NanoOK: NanoOK/1.33-intel-2017.u2-Java-9 NanoOK (pronounced na-nook) is a tool for extraction, alignment and analysis of Nanopore reads. NanoOK will extract reads as FASTA or FASTQ files, align them (with a choice of alignment tools), then generate a comprehensive multi-page PDF report containing yield, accuracy and quality analysis. NiBabel: NiBabel/2.1.0-intel-2016.u3-Python-2.7.9-freetype-2.6.5 NiBabel provides read/write access to some common medical and neuroimaging file formats, including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, MINC1, MINC2, MGH and ECAT as well as Philips PAR/REC. We can read and write Freesurfer geometry, and read Freesurfer morphometry and annotation files. There is some very limited support for DICOM. NiBabel is the successor of PyNIfTI. - Homepage: https://nipy.github.io/nibabel Nilearn: Nilearn/0.1.3-intel-2016.u3-Python-2.7.9-freetype-2.6.5 Nilearn is a Python module for fast and easy statistical learning on NeuroImaging data. - Homepage: http://nilearn.github.io/ Ninja: Ninja/1.8.2-intel-2016.u3, Ninja/1.8.2-intel-2017.u2, Ninja/1.8.2-intel-2018.u4, Ninja/1.9.0-spartan_gcc-8.1.0 Ninja is a small build system with a focus on speed. OCaml: OCaml/4.01.0-intel-2017.u2 OCaml is a general purpose industrial-strength programming language with an emphasis on expressiveness and safety. Developed for more than 20 years at Inria it benefits from one of the most advanced type systems and supports functional, imperative and object-oriented styles of programming. OPARI2: OPARI2/1.1.1-goolf-2015a, OPARI2/1.1.2-goolf-2015a, OPARI2/2.0-goolf-2015a OPARI2, the successor of Forschungszentrum Juelich's OPARI, is a source-to-source instrumentation tool for OpenMP and hybrid codes. It surrounds OpenMP directives and runtime library calls with calls to the POMP2 measurement interface. OPERA-MS: OPERA-MS/14Dec2018-spartan_gcc-6.2.0 OPERA-MS is a hybrid metagenomic assembler which combines the advantages of short and long-read technologies to provide high quality assemblies, addressing issues of low contiguity for short-read only assemblies, and low base-pair quality for long-read only assemblies. ORCA: ORCA/3_0_2-linux_x86-64-OpenMPI-1.6.5, ORCA/3_0_3-linux_x86-64-OpenMPI-1.6.5, ORCA/4_0_0-linux_x86-64-OpenMPI-2.0.2, ... OTF: OTF/1.12.4-goolf-2015a The Open Trace Format is a highly scalable, memory efficient event trace data format plus support library. It is the standard trace format for Vampir, and is open for other tools. NOW OBSOLETE: use OTF2 OTF2: OTF2/1.2.1-goolf-2015a, OTF2/2.0-goolf-2015a The Open Trace Format 2 is a highly scalable, memory efficient event trace data format plus support library. It will become the new standard trace format for Scalasca, Vampir, and Tau and is open for other tools. Octave: Octave/3.8.2-goolf-2015a, Octave/4.2.1-goolf-2015a Octopus: Octopus/9.1-intel-2017.u2, Octopus/9.1-spartan_intel-2017.u2 octopus is a software package for performing Kohn–Sham density functional theory (DFT) and time-dependent density functional theory (TDDFT) calculations. OlaFlow: OlaFlow/20170725-intel-2016.u3-OpenFOAM-4.0, OlaFlow/20170725-intel-2017.u2-OpenFOAM-5.0 This free and open source project is committed to bringing the latest advances in the simulation of wave dynamics to the OpenFOAM® and FOAM-extend communities. olaFlow includes a set of solvers and boundary conditions to generate and absorb water waves actively at the boundaries and to simulate their interaction with porous coastal structures. OpenBLAS: OpenBLAS/0.2.9-GCC-6.2.0-LAPACK-3.5.0, OpenBLAS/0.2.14-gompi-2015a-LAPACK-3.5.0, OpenBLAS/0.2.15-GCC-4.9.2-LAPACK-3.5.0, ... OpenBUGS: OpenBUGS/3.2.3 BUGS is a software package for performing Bayesian inference Using Gibbs Sampling. - Homepage: http://www.openbugs.net/ OpenCV: OpenCV/3.1.0-GCC-4.9.2, OpenCV/3.1.0-intel-2016.u3, OpenCV/3.1.0-intel-2017.u2 OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products. OpenEXR: OpenEXR/2.2.0-intel-2016.u3 OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic for use in computer imaging applications - Homepage: http://www.openexr.com/ OpenFAST: OpenFAST/2.4.0-spartan_intel-2017.u2 OpenFAST is a wind turbine simulation tool which builds on FAST v8. OpenFOAM: OpenFOAM/v1806-intel-2017.u2, OpenFOAM/2.1.1-gompi-GCC-4.6.4-OpenMPI-1.8.4, OpenFOAM/2.1.1-iompi-2016.u3-custom, ... OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. - Homepage: http://www.openfoam.com/ OpenFOAM-Extend: OpenFOAM-Extend/4.0-spartan_gcc-6.2.0-Python-2.7.13-custom, OpenFOAM-Extend/4.0-spartan_gcc-6.2.0-Python-2.7.13, ... OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. OpenImageIO: OpenImageIO/1.6.17-intel-2016.u3 OpenImageIO is a library for reading and writing images, and a bunch of related classes, utilities, and applications. - Homepage: http://openimageio.org/ OpenJPEG: OpenJPEG/2.3.1-intel-2017.u2 OpenMM: OpenMM/7.2.1-intel-2017.u2-Python-3.6.1 OpenMM is a toolkit for molecular simulation. OpenMPI: OpenMPI/1.6.5-GCC-4.9.2, OpenMPI/1.6.5-intel-2017.u2, OpenMPI/1.8.4-GCC-4.6.4, OpenMPI/1.8.4-GCC-4.9.2, ... The Open MPI Project is an open source MPI-2 implementation. OpenPGM: OpenPGM/5.2.122-intel-2016.u3, OpenPGM/5.2.122-spartan_intel-2017.u2 OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM) specification in RFC 3208 available at www.ietf.org. PGM is a reliable and scalable multicast protocol that enables receivers to detect loss, request retransmission of lost data, or notify an application of unrecoverable loss. PGM is a receiver-reliable protocol, which means the receiver is responsible for ensuring all data is received, absolving the sender of reception responsibility. - Homepage: http://code.google.com/p/openpgm/ OpenSSL: OpenSSL/1.0.1p-GCC-4.9.2, OpenSSL/1.0.1p-GCC-4.9.3, OpenSSL/1.0.2l-foss-2017b, OpenSSL/1.0.2l-GCC-4.9.2, ... OpenSim: OpenSim/4.0-GCC-6.2.0 High-performance C++ multibody dynamics/physics library for simulating articulated biomechanical and mechanical systems like vehicles, robots, and the human skeleton. OrfM: OrfM/0.7.1-goolf-2015a A simple and not slow open reading frame (ORF) caller. PAGAN: PAGAN/20150723-intel-2017.u2 PAGAN is a general-purpose method for the alignment of sequence graphs. PAGAN is based on the phylogeny-aware progressive alignment algorithm and uses graphs to describe the uncertainty in the presence of characters at certain sequence positions. However, graphs also allow describing the uncertainty in input sequences and modelling e.g. homopolymer errors in Roche 454 reads, or representing inferred ancestral sequences against which other sequences can then be aligned. PAML: PAML/4.9a-intel-2016.u3 PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. PAPI: PAPI/5.2.0-gompi-2015a, PAPI/5.2.0-goolf-2015a, PAPI/5.4.3-goolf-2015a PAPI provides the tool designer and application engineer with a consistent interface and methodology for use of the performance counter hardware found in most major microprocessors. PAPI enables software engineers to see, in near real time, the relation between software performance and processor events. In addition Component PAPI provides access to a collection of components that expose performance measurement opportunites across the hardware and software stack. PARCAS: PARCAS/20181017-GCC-4.9.2 PCMSolver: PCMSolver/1.1.5-intel-2016.u3-Python-2.7.9 PCRE: PCRE/8.36-GCC-4.9.2, PCRE/8.36-GCC-6.2.0, PCRE/8.36-gompi-2015a, PCRE/8.36-goolf-2015a, PCRE/8.36-intel-2016.u3, ... PDT: PDT/3.19-goolf-2015a, PDT/3.22-goolf-2015a, PDT/3.25-goolf-2015a Program Database Toolkit (PDT) is a framework for analyzing source code written in several programming languages and for making rich program knowledge accessible to developers of static and dynamic analysis tools. PDT implements a standard program representation, the program database (PDB), that can be accessed in a uniform way through a class library supporting common PDB operations. PEAR: PEAR/0.9.6-intel-2017.u2, PEAR/0.9.11-foss-2017b, PEAR/0.9.11-GCC-6.2.0, PEAR/0.9.11-intel-2018.u4 PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory. PEST: PEST/15-GCC-6.2.0 Model-Independent Parameter Estimation and Uncertainty Analysis PEST-plproc: PEST-plproc/3.0-intel-2017.u2 PLPROC is a “parameter list processor”. It was written to expedite the use of PEST in conjunction with complex spatial models which may possess structured or unstructured grids. PETSc: PETSc/3.5.3-intel-2016.u3-Python-2.7.9, PETSc/3.6.3-intel-2016.u3-Python-2.7.9, PETSc/3.6.3-intel-2016.u3-Python-2.7.11-test, ... PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. PGI: PGI/16.10-GCC-4.9.2-2.26, PGI/16.10-GCC-5.4.0-2.26, PGI/16.10-GCC-6.2.0-2.26, PGI/17.10-GCC-4.9.2-2.26, PGI/17.10-GCC-5.4.0-2.26, ... C, C++ and Fortran compilers from The Portland Group - PGI PIL: PIL/1.1.7-intel-2016.u3-Python-2.7.9-freetype-2.6.5, PIL/1.1.7-intel-2016.u3-Python-2.7.11-freetype-2.6.3, ... The Python Imaging Library (PIL) adds image processing capabilities to your Python interpreter. This library supports many file formats, and provides powerful image processing and graphics capabilities. - Homepage: http://www.pythonware.com/products/pil PLINK: PLINK/1.07-x86_64, PLINK/1.90-b5.3-x86-64 plink-1.07-src: Whole-genome association analysis toolset PLUMED: PLUMED/2.5.0-spartan_gcc-6.2.0-cuda9.2-Python-3.7.3 PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. PLY: PLY/3.8-intel-2016.u3-Python-2.7.9, PLY/3.8-intel-2016.u3-Python-2.7.11, PLY/3.11-spartan_gcc-8.1.0-Python-3.7.3 PLY is yet another implementation of lex and yacc for Python. POI: POI/3.17-20170915-x86_64 The Apache POI Project's mission is to create and maintain Java APIs for manipulating various file formats based upon the Office Open XML standards (OOXML) and Microsoft's OLE 2 Compound Document format (OLE2). In short, you can read and write MS Excel files using Java. In addition, you can read and write MS Word and MS PowerPoint files using Java. Apache POI is your Java Excel solution (for Excel 97-2008). We have a complete API for porting other OOXML and OLE2 formats and welcome others to participate. PRANK: PRANK/140110-GCC-4.9.2, PRANK/140110-intel-2016.u3, PRANK/170427-intel-2017.u2, PRANK/170427-spartan_gcc-6.2.0, ... PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences. PRANK is based on a novel algorithm that treats insertions correctly and avoids over-estimation of the number of deletion events. PROJ: PROJ/4.8.0-intel-2016.u3, PROJ/4.9.2-GCC-4.9.2, PROJ/4.9.3-GCC-4.9.2, PROJ/4.9.3-GCC-6.2.0, PROJ/4.9.3-intel-2016.u3, ... Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates PaStiX: PaStiX/5.2.2.22-intel-2016.u3 PaStiX (Parallel Sparse matriX package) is a scientific library that provides a high performance parallel solver for very large sparse linear systems based on direct methods. - Homepage: http://pastix.gforge.inria.fr/ Pango: Pango/1.40.0-intel-2016.u3, Pango/1.40.6-foss-2017b, Pango/1.40.6-GCC-4.9.2, Pango/1.40.6-GCC-6.2.0, ... Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x. - Homepage: http://www.pango.org/ ParMETIS: ParMETIS/3.2.0-goolf-2015a, ParMETIS/3.2.0-intel-2016.u3-test, ParMETIS/3.2.0-intel-2016.u3, ParMETIS/3.2.0-intel-2017.u2, ... ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes. - Homepage: http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview ParMGridGen: ParMGridGen/1.0-spartan_gcc-6.2.0, ParMGridGen/1.0-spartan_intel-2017.u2 ParMGridGen is an MPI-based parallel library that is based on the serial package MGridGen, that implements (serial) algorithms for obtaining a sequence of successive coarse grids that are well-suited for geometric multigrid methods. ParaView: ParaView/4.4.0-spartan_intel-2017.u2-mpi, ParaView/5.3.0-spartan_intel-2017.u2-mpi, ... Paraview is a scientific parallel visualizer Paraview: Paraview/4.4.0-intel-2016.u3, Paraview/5.1.2-intel-2016.u3-mpi, Paraview/5.2.0-intel-2016.u3-mpi, ... Paraview is a scientific parallel visualizer - Homepage: http://www.paraview.org Parse-Yapp: Parse-Yapp/1.05-intel-2016.u3-Perl-5.20.0 A perl frontend to the Parse::Yapp module PartitionFinder: PartitionFinder/1.1.1, PartitionFinder/2.0.0-pre9 Perl: Perl/5.16.3-goolf-2015a, Perl/5.20.0-GCC-4.9.2, Perl/5.20.0-GCC-4.9.3, Perl/5.20.0-goolf-2015a, Perl/5.20.0-intel-2016.u3-bare, ... Larry Wall's Practical Extraction and Report Language - Homepage: http://www.perl.org/ PhyML: PhyML/3.1, PhyML/3.3.20190321-foss-2017b-phrex, PhyML/3.3.20190321-foss-2017b-mpi Piggy: Piggy/1.4-spartan_intel-2017.u2 Piggy is a tool for analysing the intergenic component of bacterial genomes. Pillow: Pillow/2.8.1-intel-2016.u3-Python-2.7.9, Pillow/2.8.1-intel-2016.u3-Python-2.7.10, Pillow/2.8.1-intel-2016.u3-Python-3.5.2, ... Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors. Pillow-simd: Pillow-simd/5.4.1-intel-2017.u2-GCC-6.2.0-CUDA9-Python-3.6.4, ... Pillow-SIMD is "following" Pillow. Pillow-SIMD versions are 100% compatible drop-in replacements for Pillow of the same version. Platypus: Platypus/20180622-GCC-6.2.0 The Platypus variant caller. PnetCDF: PnetCDF/1.9.0-foss-2017b, PnetCDF/1.11.2-spartan_gcc-6.2.0, PnetCDF/1.11.2-spartan_intel-2017.u2 Parallel netCDF: A Parallel I/O Library for NetCDF File Access PoPoolation2: PoPoolation2/1.201 PoPoolation2 allows to compare allele frequencies for SNPs between two or more populations and to identify significant differences. PoPoolation2 requires next generation sequencing data of pooled genomic DNA (Pool-Seq). It may be used for measuring differentiation between populations, for genome wide association studies and for experimental evolution. Polkit: Polkit/0.107-GCC-6.2.0 polkit is an application-level toolkit for defining and handling the policy that allows unprivileged processes to speak to privileged processes: It is a framework for centralizing the decision making process with respect to granting access to privileged operations for unprivileged applications. PopPUNK: PopPUNK/1.1.3-intel-2017.u2-Python-3.6.4 PopPUNK (POPulation Partitioning Using Nucleotide Kmers) Porechop: Porechop/0.2.4-intel-2017.u2-Python-3.6.4 Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. PostgreSQL: PostgreSQL/9.3.5-goolf-2015a, PostgreSQL/9.3.5-intel-2016.u3 PostgreSQL is a powerful, open source object-relational database system. It is fully ACID compliant, has full support for foreign keys, joins, views, triggers, and stored procedures (in multiple languages). It includes most SQL:2008 data types, including INTEGER, NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. It also supports storage of binary large objects, including pictures, sounds, or video. It has native programming interfaces for C/C++, Java, .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation. Prodigal: Prodigal/2.6.3-intel-2017.u2, Prodigal/2.60-intel-2016.u3 Prodigal (PROkaryotic DynamIc programming Genefinding ALgorithm) is an open source lightweight microbial genefinding program developed at University of Tennessee and Oak Ridge National Laboratory.. Prokka: Prokka/1.13-intel-2016.u3-BioPerl-1.6.924, Prokka/1.13-intel-2017.u2-BioPerl-1.7.2 Prokka is a software tool for the rapid annotation of prokaryotic genomes. PyAMG: PyAMG/3.0.1-intel-2017.u2-Python-3.6.1 PyAMG is a library of Algebraic Multigrid (AMG) solvers with a convenient Python interface. PyCharm: PyCharm/2019.3.1 PyCharm Community Edition: Python IDE for Professional Developers PyMesh: PyMesh/0.2.1-spartan_gcc-6.2.0-Python-3.7.3 Geometry Processing Library for Python PyOpenGL: PyOpenGL/3.0.1-intel-2016.u3-Python-2.7.9 PyOpenGL is the most common cross platform Python binding to OpenGL and related APIs. The binding is created using the standard ctypes library, and is provided under an extremely liberal BSD-style Open-Source license. PyQt: PyQt/4.11.4-intel-2016.u3-Python-2.7.9, PyQt/4.11.4-intel-2016.u3-Python-2.7.10, PyQt/4.11.4-intel-2016.u3-Python-2.7.11, ... PyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework. PyTables: PyTables/3.4.2-intel-2017.u2-Python-3.6.4 PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browse, process and search very large amounts of data. One important feature of PyTables is that it optimizes memory and disk resources so that data takes much less space (specially if on-flight compression is used) than other solutions such as relational or object oriented databases. PyTorch: PyTorch/0.3.1-intel-2017.u2-GCC-5.4.0-CUDA8-Python-3.5.2-GPU, PyTorch/0.4.0-intel-2017.u2-GCC-6.2.0-CUDA9-Python-3.5.2-GPU, ... PyTorch is a deep learning framework that puts Python first. PyVCF: PyVCF/0.6.8-Python-2.7.10 PyVCF is a VCFv4.0 and 4.1 parser for Python. This is a bundle of PyVCF, which includes dependencies pbr, linecache2, and whatever else comes up. PyYAML: PyYAML/3.12-intel-2017.u2-GCC-6.2.0-CUDA9-Python-3.6.4, PyYAML/3.12-intel-2017.u2-GCC-6.2.0-CUDA10-Python-3.6.4, ... PyYAML is a YAML parser and emitter for the Python programming language. PyZMQ: PyZMQ/14.7.0-intel-2016.u3-Python-2.7.9-zmq3, PyZMQ/15.2.0-intel-2016.u3-Python-3.5.2-zmq3, ... Python bindings for ZeroMQ - Homepage: http://www.zeromq.org/bindings:python Pygments: Pygments/2.0.2-intel-2016.u3-Python-2.7.9, Pygments/2.0.2-spartan_intel-2017.u2-Python-2.7.13 Generic syntax highlighter suitable for use in code hosting, forums, wikis or other applications that need to prettify source code. - Homepage: http://pygments.org/ Pysam: Pysam/0.14-intel-2017.u2-Python-3.6.4, Pysam/0.15.1-GCC-6.2.0-Python-2.7.13, ... Pysam is a python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix. Python: Python/2.7.9-GCC-4.9.2-bare, Python/2.7.9-GCC-4.9.2, Python/2.7.9-goolf-2015a, Python/2.7.9-intel-2016.u3-test, ... Python is a programming language that lets you work more quickly and integrate your systems more effectively. PythonBundle: PythonBundle/2.7.10-intel-2016.u3 Python is a programming language that lets you work more quickly and integrate your systems more effectively. Pyvolve: Pyvolve/0.8.2-intel-2016.u3-Python-2.7.10 Pyvolve is an open-source Python module for simulating sequences along a phylogenetic tree according to continuous-time Markov models of sequence evolution. QIIME: QIIME/1.8.0-intel-2016.u3-Python-2.7.10, QIIME/1.9.1-GCC-4.9.2-Python-2.7.11 QIIME consists of native Python 2 code and additionally wraps many external applications. This gives the user flexibility to easily build their own analysis pipelines, making use of popular microbial community analysis tools. QIIME handles the processing of input and output of these applications, so the user can spend time analyzing their data rather than parsing, writing, and converting file formats. QIIME2: QIIME2/2018.2, QIIME2/2019.1-Miniconda3-4.5.4, QIIME2/2019.1 QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data. QUAST: QUAST/4.3-intel-2016.u3, QUAST/4.5-intel-2017.u2 QUAST performs fast and convenient quality evaluation and comparison of genome assemblies. Qhull: Qhull/2015.2-goolf-2015a, Qhull/2015.2-intel-2016.u3, Qhull/2015.2-intel-2017.u2 Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull. Qt: Qt/3.3.8-intel-2017.u2-GCC-6.2.0-CUDA9, Qt/3.3.8-spartan_gcc-8.1.0, Qt/4.8.2-iomkl-2016.u3, Qt/4.8.6-GCC-4.9.2, ... Qt is a comprehensive cross-platform C++ application framework. Qt5: Qt5/5.7.0-intel-2016.u3, Qt5/5.7.0-intel-2017.u2, Qt5/5.7.0-spartan_intel-2017.u2, Qt5/5.10.1-foss-2017b, ... Qt is a comprehensive cross-platform C++ application framework. QuaZip: QuaZip/0.8.1-intel-2017.u2 QuaZIP is a simple C++ wrapper around Minizip. Qualimap: Qualimap/2.2.1-Java-1.8.0_152 Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts. QuantumESPRESSO: QuantumESPRESSO/5.4.0-intel-2016.u3, QuantumESPRESSO/6.1-intel-2016.u3, QuantumESPRESSO/6.3-intel-2017.u2 Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft). - Homepage: http://www.pwscf.org/ Qwt: Qwt/6.1.3-intel-2017.u2, Qwt/6.1.4-spartan_gcc-6.2.0, Qwt/6.1.4-spartan_gcc-8.1.0, Qwt/6.1.4-spartan_intel-2017.u2 The Qwt library contains GUI Components and utility classes which are primarily useful for programs with a technical background. R: R/2.15.3-GCC-4.9.2, R/3.2.1-GCC-4.9.2, R/3.2.1-intel-2016.u3, R/3.2.3-intel-2016.u3, R/3.4.0-GCC-4.9.2, R/3.4.0-intel-2017.u2, ... R is a free software environment for statistical computing and graphics. - Homepage: http://www.r-project.org/ R-bundle-Bioconductor: R-bundle-Bioconductor/3.7-GCC-6.2.0-R-3.5.0, R-bundle-Bioconductor/3.7-intel-2017.u2-R-3.5.0, ... R is a free software environment for statistical computing and graphics. RAxML: RAxML/7.7.5-intel-2016.u3-hybrid-sse3, RAxML/7.7.5-intel-2016.u3-mpi-sse3, RAxML/7.7.5-intel-2016.u3-mt-sse3, ... REforge: REforge/20200207-spartan_gcc-6.2.0 REforge (Regulatory Element forward genomics) is a method to associate transciption factor binding site divergence in regulatory elements with phenotypic differences between species. RNA-SeQC: RNA-SeQC/1.1.8-Java-1.8.0_71 ROOT: ROOT/6.10.08-intel-2017.u2, ROOT/6.14.06-spartan_gcc-6.2.0, ROOT/6.20.02-spartan_gcc-6.2.0-Python-3.7.3 ROOT is A modular scientific software toolkit. It provides all the functionalities needed to deal with big data processing, statistical analysis, visualisation and storage. It is mainly written in C++ but integrated with other languages such as Python and R. RSEM: RSEM/1.3.1-intel-2017.u2 RNA-Seq by Expectation-Maximization Ra: Ra/20181211-intel-2017.u2 Ra is as a fast and easy to use assembler for raw reads generated by third generation sequencing. It consists of Minimap2, Rala and Racon as depicted on figure bellow. Racon: Racon/1.3.1-GCC-6.2.0, Racon/1.3.1-intel-2016.u3, Racon/1.3.1-intel-2017.u2 Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. RapidCFD: RapidCFD/20180426-intel-2017.u2-custom, RapidCFD/20180426-intel-2017.u2 CFD toolbox running on CUDA OpenFOAM solvers ported to Nvidia CUDA. All the calculations are done on the GPU giving a huge speed-up. Still in development stage, waiting for your contribution! Rcorrector: Rcorrector/1.0.2-spartan_intel-2017.u2, Rcorrector/1.0.4-spartan_intel-2017.u2 Rcorrector(RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data. RedDog: RedDog/V1beta11-intel-2016.u3-Python-2.7.10 This program implements a workflow pipeline for short read length sequencing analysis, including the read mapping task, through to variant detection, followed by analyses (SNPs only). Relion: Relion/2.0.3-intel-2016.u3, Relion/2.0.3-intel-2017.u2-GCC-6.2.0-CUDA9, Relion/3-beta-intel-2016.u3, ... RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM). - Homepage: http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page Rmpi: Rmpi/0.6-9-spartan_gcc-6.2.0 An interface (wrapper) to MPI. Roary: Roary/3.12.0-spartan_intel-2017.u2-Perl-5.26.0 Rapid large-scale prokaryote pan genome analysis Rubra: Rubra/20150505-intel-2016.u3-Python-2.7.10 Rubra is a bioinformatics pipeline. Ruby: Ruby/2.4.1-GCC-4.9.2, Ruby/2.4.1-intel-2016.u3, Ruby/2.4.1-intel-2017.u2 Ruby is a dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write. Rust: Rust/1.8.0-goolf-2015a, Rust/1.20.0-goolf-2015a, Rust/1.30.0 Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety. S-Lang: S-Lang/2.3.0-GCC-4.9.2 S-Lang is a multi-platform programmer's library designed to allow a developer to create robust multi-platform software. It provides facilities required by interactive applications such as display/screen management, keyboard input, keymaps, and so on. SAGE: SAGE/6.4 S.A.G.E. (Statistical Analysis for Genetic Epidemiology) is free software package containing programs for use in the genetic analysis of family, pedigree and individual data. - Homepage: http://darwin.cwru.edu/sage/ SAMblaster: SAMblaster/0.1.22-GCC-4.9.2, SAMblaster/0.1.22-intel-2016.u3 SAMtools: SAMtools/0.1.18-GCC-4.9.2, SAMtools/0.1.18-intel-2016.u3, SAMtools/0.1.19-GCC-4.9.2, SAMtools/0.1.19-intel-2016.u3, ... SCALCE: SCALCE/2.7-GCC-4.9.2 SCALCE [skeɪlz] is a FASTQ compression tool that uses locally consistet parsing to obtain better compression rate. SCALCE has been specifically designed for Illumina reads but it can handle other technologies (that generate base pair reads) if the read length is the same throughout the file. SCIP: SCIP/3.2.1-intel-2016.u3 SCIP is currently one of the fastest non-commercial solvers for mixed integer programming (MIP) and mixed integer nonlinear programming (MINLP). It is also a framework for constraint integer programming and branch-cut-and-price. It allows for total control of the solution process and the access of detailed information down to the guts of the solver. - Homepage: http://scip.zib.de/ SCOOP: SCOOP/0.7.1.1-intel-2016.u3-Python-3.5.2 SCOOP (Scalable COncurrent Operations in Python) is a distributed task module allowing concurrent parallel programming on various environments, from heterogeneous grids to supercomputers. SCOTCH: SCOTCH/6.0.0_esmumps-intel-2017.u2, SCOTCH/6.0.4-foss-2017b, SCOTCH/6.0.4-goolf-2015a, SCOTCH/6.0.4-intel-2016.u3, ... Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning. - Homepage: http://gforge.inria.fr/projects/scotch/ SCons: SCons/2.3.6-GCC-4.9.2-Python-2.7.9, SCons/2.3.6-intel-2016.u3-Python-2.7.11, SCons/2.3.6-intel-2017.u2-Python-2.7.11, ... SCons is a software construction tool. - Homepage: http://www.scons.org/ SDL: SDL/1.2.15-intel-2017.u2-GCC-6.2.0-CUDA9 SDL: Simple DirectMedia Layer, a cross-platform multimedia library SDL2: SDL2/2.0.9-intel-2017.u2-GCC-6.2.0-CUDA9 SDL: Simple DirectMedia Layer, a cross-platform multimedia library SDL2_gfx: SDL2_gfx/2.0.4-intel-2017.u2-GCC-6.2.0-CUDA9 SDL: Simple DirectMedia Layer, a cross-platform multimedia library SDL2_image: SDL2_image/2.0.4-intel-2017.u2-GCC-6.2.0-CUDA9 SDL: Simple DirectMedia Layer, a cross-platform multimedia library SDL2_ttf: SDL2_ttf/2.0.15-intel-2017.u2-GCC-6.2.0-CUDA9 SDL: Simple DirectMedia Layer, a cross-platform multimedia library SDL_SGE: SDL_SGE/20170501-intel-2017.u2-GCC-6.2.0-CUDA9 SGE is a graphics library for the Simple Direct Media Layer. SGE provides pixel operations, graphics primitives, TrueType rendering, rotation&scaling, and much more. SEPP: SEPP/4.3.10-spartan_intel-2017.u2-Python-3.6.4 This repository includes code for SEPP, TIPP, UPP, HIPPI. The three methods use ensembles of Hidden Markov Models (HMMs) in different ways, each focusing on a different problem. Each of these related tools has its own README file. SIONlib: SIONlib/1.6.1-goolf-2015a-tools, SIONlib/1.6.1-goolf-2015a SIONlib is a scalable I/O library for parallel access to task-local files. The library not only supports writing and reading binary data to or from several thousands of processors into a single or a small number of physical files, but also provides global open and close functions to access SIONlib files in parallel. This package provides a stripped-down installation of SIONlib for use with performance tools (e.g., Score-P), with renamed symbols to avoid conflicts when an application using SIONlib itself is linked against a tool requiring a different SIONlib version. SIP: SIP/4.16.8-intel-2016.u3-Python-2.7.10, SIP/4.18-intel-2016.u3-Python-2.7.9, SIP/4.18-intel-2016.u3-Python-2.7.10, ... SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries. SKESA: SKESA/2.3.0-spartan_intel-2017.u2 SKESA is a de-novo sequence read assembler for cultured single isolate genomes based on DeBruijn graphs. SLEPc: SLEPc/3.6.2-intel-2016.u3-Python-2.7.9, SLEPc/3.6.2-intel-2016.u3-Python-2.7.11, SLEPc/3.11.1-spartan_gcc-8.1.0 SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems. SLiM: SLiM/3.3.1-GCC-4.9.2 SLiM is an evolutionary simulation framework that combines a powerful engine for population genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios. SMRT-Link: SMRT-Link/8.0.0.79519-cli-tools-only PacBio’s open-source SMRT Analysis software suite is designed for use with Single Molecule, Real-Time (SMRT) Sequencing data. You can analyze, visualize, and manage your data through an intuitive GUI or command-line interface. You can also integrate SMRT Analysis in your existing data workflow through the extensive set of APIs provided SOLAR-Eclipse: SOLAR-Eclipse/8.1.1 SPAdes: SPAdes/3.8.1-GCC-4.9.2-Python-3.5.2, SPAdes/3.10.1-GCC-4.9.2-Python-3.5.2, SPAdes/3.11.1-GCC-4.9.2-Python-3.5.2, ... Genome assembler for single-cell and isolates data sets SPM: SPM/12-GCC-4.7.4, SPM/12-GCC-6.2.0-MATLAB-2018b Statistical Parametric Mapping refers to the construction and assessment of spatially extended statistical processes used to test hypotheses about functional imaging data. These ideas have been instantiated in software that is called SPM. The SPM software package has been designed for the analysis of brain imaging data sequences. The sequences can be a series of images from different cohorts, or time-series from the same subject. The current release is designed for the analysis of fMRI, PET, SPECT, EEG and MEG. - Homepage: http://www.fil.ion.ucl.ac.uk/spm/ SPSS: SPSS/25 SQLite: SQLite/3.8.8.1-GCC-4.9.2, SQLite/3.8.8.1-intel-2016.u3, SQLite/3.8.11.1-GCC-4.9.2, SQLite/3.8.11.1-intel-2016.u3, ... SQLite: SQL Database Engine in a C Library - Homepage: http://www.sqlite.org/ SRA-Toolkit: SRA-Toolkit/2.5.4-centos_linux64, SRA-Toolkit/2.8.1-2-centos_linux64, SRA-Toolkit/2.8.2-1-centos_linux64, ... The NCBI SRA Toolkit enables reading (dumping) of sequencing files from the SRA database and writing (loading) files into the .sra format SRST2: SRST2/0.2.0-intel-2017.u2-Python-2.7.13 Short Read Sequence Typing for Bacterial Pathogens -- This program is designed to take Illumina sequence data, a MLST database and/or a database of gene sequences (e.g. resistance genes, virulence genes, etc) and report the presence of STs and/or reference genes. SSPACE_Basic: SSPACE_Basic/2.1.1-GCC-6.2.0-Perl-5.20.3 SSPACE Basic, SSAKE-based Scaffolding of Pre-Assembled Contigs after Extension STAR: STAR/2.5.3a-intel-2016.u3, STAR/2.6.0c-intel-2018.u4, STAR/2.7.3a-intel-2017.u2, STAR/2.7.3a-intel-2019.u4 STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays. - Homepage: https://github.com/alexdobin/STAR SUMO: SUMO/0.31.0-GCC-4.9.2 "Simulation of Urban MObility" (SUMO) is an open source, highly portable, microscopic and continuous road traffic simulation package designed to handle large road networks. - Homepage: http://sumo.dlr.de/wiki/Simulation_of_Urban_MObility_-_Wiki SUNDIALS: SUNDIALS/2.7.0-intel-2016.u3, SUNDIALS/2.7.0-spartan_gcc-8.1.0, SUNDIALS/3.1.0-intel-2016.u3 SUNDIALS is a SUite of Nonlinear and DIfferential/ALgebraic equation Solvers. It consists of the following six solvers: CVODE, solves initial value problems for ordinary differential equation (ODE) systems; CVODES, solves ODE systems and includes sensitivity analysis capabilities (forward and adjoint); ARKODE, solves initial value ODE problems with additive Runge-Kutta methods, include support for IMEX methods; IDA, solves initial value problems for differential-algebraic equation (DAE) systems; IDAS, solves DAE systems and includes sensitivity analysis capabilities (forward and adjoint); KINSOL, solves nonlinear algebraic systems. SUPER-FOCUS: SUPER-FOCUS/0.33-intel-2017.u2-Python-3.6.4 A super-fast templating language that borrows the best ideas from the existing templating languages SVE: SVE/0.1.0-GCC-6.2.0 SVE is a python script based execution engine for Structural Variation (SV) detection and can be used for any levels of data inputs, raw FASTQs, aligned BAMs, or variant call format (VCFs), and generates a unified VCF as its output. By design, SVE consists of alignment, realignment and the ensemble of state-of-the-art SV-calling algorithms by default. They are BreakDancer, BreakSeq, cnMOPS, CNVnator, DELLY, Hydra and LUMPY. FusorSV is also embedded that is a data mining approach to assess performance and merge callsets from an ensemble of SV-calling algorithms. SWASH: SWASH/3.14-intel-2016.u3-mt SWASH is a general-purpose numerical tool for simulating unsteady, non-hydrostatic, free-surface, rotational flow and transport phenomena in coastal waters as driven by waves, tides, buoyancy and wind forces. - Homepage: http://swash.sourceforge.net/ SWIG: SWIG/3.0.11-goolf-2015a-Python-2.7.12, SWIG/3.0.11-intel-2016.u3-Python-2.7.9, SWIG/3.0.11-intel-2016.u3-Python-2.7.11, ... SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages. SaTScan: SaTScan/9.6 SaTScan(TM) is a free software that analyzes spatial, temporal and space-time data using the spatial, temporal, or space-time scan statistics. Sablotron: Sablotron/1.0.3-goolf-2015a Sablotron XML processor - Homepage: http://sablotron.sourceforge.net/ Sagemath: Sagemath/8.1 SageMath is a free open-source mathematics software system licensed under the GPL. It builds on top of many existing open-source packages. Salmon: Salmon/0.11.3 Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. ScaLAPACK: ScaLAPACK/2.0.2-gompi-2015a-OpenBLAS-0.2.14-LAPACK-3.5.0, ScaLAPACK/2.0.2-gompi-2016b-OpenBLAS-0.2.18-LAPACK-3.5.0, ... ScientificPython: ScientificPython/2.9.4-goolf-2015a-Python-2.7.10, ScientificPython/2.9.4-intel-2016.u3-Python-2.7.9, ... ScientificPython is a collection of Python modules for scientific computing. It contains support for geometry, mathematical functions, statistics, physical units, IO, visualization, and parallelization. Scipion: Scipion/1.2-GCC-6.2.0-CUDA-9.custom, Scipion/1.2-GCC-6.2.0-CUDA-9, Scipion/1.2-GCC-6.2.0, Scipion/1.2.1-GCC-6.2.0-CUDA-9.0, ... Scipion is an image processing framework to obtain 3D models of macromolecular complexes using Electron Microscopy. Score-P: Score-P/2.0.1-goolf-2015a The Score-P measurement infrastructure is a highly scalable and easy-to-use tool suite for profiling, event tracing, and online analysis of HPC applications. Seaborn: Seaborn/0.8.1-intel-2017.u2-Python-2.7.11, Seaborn/0.8.1-intel-2017.u2-Python-2.7.13 Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics. Seqtk: Seqtk/1.3-r106-foss-2017b, Seqtk/1.3-r106-GCCcore-6.4.0, Seqtk/1.3-r106-intel-2017.u2, Seqtk/1.3-r106-spartan_gcc-6.2.0, ... Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. Serf: Serf/1.3.8-GCC-4.9.2, Serf/1.3.9-GCC-6.2.0, Serf/1.3.9-spartan_intel-2017.u2 The serf library is a high performance C-based HTTP client library built upon the Apache Portable Runtime (APR) library - Homepage: http://serf.apache.org/ Simbody: Simbody/3.6.1-GCC-6.2.0 High-performance C++ multibody dynamics/physics library for simulating articulated biomechanical and mechanical systems like vehicles, robots, and the human skeleton. Singularity: Singularity/2.6.1-intel-2017.u2, Singularity/3.2.0-spartan_gcc-6.2.0, Singularity/3.5.3-spartan_gcc-6.2.0 Singularity is a portable application stack packaging and runtime utility. Snippy: Snippy/4.3.6-intel-2017.u2, Snippy/4.3.6-spartan_intel-2017.u2 Assemble bacterial isolate genomes from Illumina paired-end reads. Spark: Spark/1.6.2 Sphinx: Sphinx/1.3.3-intel-2016.u3-Python-2.7.9, Sphinx/1.3.3-intel-2016.u3-Python-2.7.11 Sphinx is a tool that makes it easy to create intelligent and beautiful documentation. It was originally created for the new Python documentation, and it has excellent facilities for the documentation of Python projects, but C/C++ is already supported as well, and it is planned to add special support for other languages as well. - Homepage: http://sphinx.pocoo.org/ Spidermonkey: Spidermonkey/1.0.0-GCC-6.2.0 SpiderMonkey is Mozilla's JavaScript engine written in C and C++. It is used in various Mozilla products, including Firefox, and is available under the MPL2. Stacks: Stacks/2.3e-GCC-6.2.0, Stacks/2.3-GCC-6.2.0, Stacks/2.3-spartan_gcc-6.2.0 Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography. Stata: Stata/12, Stata/15 Stata is a complete, integrated statistical software package that provides everything you need for data analysis, data management, and graphics. - Homepage: http://www.stata.com/support/updates/ StringTie: StringTie/1.3.3b-intel-2016.u3 StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. - Homepage: https://ccb.jhu.edu/software/stringtie/#contact Structure: Structure/2.3.4-GCC-6.2.0, Structure/2.3.4-intel-2016.u3 The program structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. It can be applied to most of the commonly-used genetic markers, including SNPS, microsatellites, RFLPs and AFLPs. Subread: Subread/1.5.1-GCC-4.9.2, Subread/1.6.3-GCC-8.2.0, Subread/1.6.3-intel-2018.u4 Subversion: Subversion/1.8.14-GCC-4.9.2, Subversion/1.10.4-spartan_intel-2017.u2, Subversion/1.12.0-GCC-6.2.0, ... Subversion is an open source version control system. SuiteSparse: SuiteSparse/3.7.1-spartan_intel-2017.u2-ParMETIS-4.0.3, SuiteSparse/4.0.0-spartan_intel-2017.u2-ParMETIS-4.0.3, ... SuiteSparse is a collection of libraries manipulate sparse matrices. Summovie: Summovie/1.0.2 Use with Unlur. Unblur is used to align the frames of movies recorded on an electron microscope to reduce image blurring due to beam-induced motion. - Homepage: http://grigoriefflab.janelia.org/unblur Szip: Szip/2.1-foss-2017b, Szip/2.1-GCC-4.9.2, Szip/2.1-GCC-5.4.0, Szip/2.1-GCC-6.2.0, Szip/2.1-PGI-16.10-GCC-5.4.0-2.26, ... TAU: TAU/2.27-goolf-2015a, TAU/2.27.1-goolf-2015a, TAU/2.27.2-goolf-2015a The TAU Performance System is a portable profiling and tracing toolkit for performance analysis of parallel programs written in Fortran, C, C++, Java, Python. TakeABreak: TakeABreak/1.1.2 TakeABreak detects inversion breakpoints without a reference genome by looking for fixed size topological patterns in the de Bruijn graph. Tcl: Tcl/8.5.7-GCC-4.9.3, Tcl/8.5.12-GCC-6.2.0, Tcl/8.5.12-intel-2016.u3, Tcl/8.5.12-intel-2017.u2, Tcl/8.5.12, Tcl/8.6.3-GCC-4.9.2, ... TensorRT: TensorRT/6.0.1.5-CUDA-9-cuDNN-7.6, TensorRT/6.0.1.5-CUDA-10.1-cuDNN-7.6 NVIDIA TensorRT is a platform for high-performance deep learning inference Tensorflow: Tensorflow/0.12.0-intel-2017.u2-Python-2.7.13-GPU, Tensorflow/0.12.1-intel-2016.u3-Python-2.7.12, ... An open-source software library for Machine Intelligence Tensorflow-CPU: Tensorflow-CPU/1.15.0-spartan_intel-2017.u2-Python-3.6.4 An open-source software library for Machine Intelligence Theano: Theano/1.0.2-intel-2017.u2-GCC-6.2.0-CUDA9-Python-3.5.2-Tensorflow-1.10.0, ... Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently. Thunar: Thunar/1.6.11-intel-2016.u3 Thunar is the Xfce file manager, a GTK+ 2 GUI to organise the files on your computer. - Homepage: xfce.org Tk: Tk/8.5.12-intel-2016.u3, Tk/8.6.3-GCC-4.9.2-no-X11, Tk/8.6.4-GCC-4.9.2-no-X11, Tk/8.6.4-intel-2016.u3-no-X11, ... Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building a graphical user interface (GUI) in many different programming languages. - Homepage: http://www.tcl.tk/ Tkinter: Tkinter/2.7.11-intel-2017.u2-Python-2.7.11, Tkinter/2.7.13-intel-2017.u2-Python-2.7.13, ... Tkinter module, built with the Python buildsystem TopHat: TopHat/2.1.0-intel-2016.u3, TopHat/2.1.1-GCC-4.9.2, TopHat/2.1.1-intel-2016.u3 Torch: Torch/20171208-cuDNN7-intel-2017.u2-GCC-5.4.0-CUDA8, Torch/20171208-intel-2017.u2-GCC-5.4.0-CUDA8-cuDNN6, ... Torch is a scientific computing framework with wide support for machine learning algorithms that puts GPUs first. It is easy to use and efficient, thanks to an easy and fast scripting language, LuaJIT, and an underlying C/CUDA implementation. TransLiG: TransLiG/1.2-spartan_intel-2017.u2, TransLiG/1.3-spartan_intel-2017.u2 TransLiG is an efficient de novo trascriptome assembler for RNA-Seq data. It can assemble all transcripts from short reads (single or paired) without using a reference. Trilinos: Trilinos/12.4.2-intel-2016.u3-Python-2.7.11, Trilinos/12.12.1-spartan_gcc-8.1.0-Python-3.7.3 The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. A unique design feature of Trilinos is its focus on packages. TrimGalore: TrimGalore/0.4.4 Trim Galore! is a wrapper script to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files (for directional, non-directional (or paired-end) sequencing). Trim_Galore: Trim_Galore/0.4.4-intel-2016.u3, Trim_Galore/0.4.4-intel-2017.u2, Trim_Galore/0.6.4-intel-2017.u2 A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. Trimmomatic: Trimmomatic/0.30, Trimmomatic/0.36-Java-1.8.0_71, Trimmomatic/0.36-Java-1.8.0_152, Trimmomatic/0.36, ... Trinity: Trinity/2.6.6-intel-2017.u2 Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads. TrinityRNAseq: TrinityRNAseq/2.5.1-intel-2017.u2 TurboVNC: TurboVNC/2.1.1-intel-2016.u3, TurboVNC/2.1.1-intel-2017.u2 TurboVNC is a high-performance, enterprise-quality version of VNC based on TightVNC, TigerVNC, and X.org . It contains a variant of Tight encoding that is tuned for maximum performance and compression with 3D applications (VirtualGL), video, and other image-intensive workloads. TurboVNC, in combination with VirtualGL, provides a complete solution for remotely displaying 3D applications with interactive performance. Please use TurboVNC server in interactive sessions (`sinteractive`) only. Note that tunnelling will be required for this. - Homepage: https://sourceforge.net/projects/turbovnc/ UCX: UCX/1.7.x-GCC-6.2.0-nocuda, UCX/1.7.x-GCC-6.2.0, UCX/1.7.x-GCCcore-8.3.0, UCX/1.8.0-GCC-6.2.0 Unified Communication X An open-source production grade communication framework for data centric and high-performance applications UDUNITS: UDUNITS/2.2.20-intel-2016.u3, UDUNITS/2.2.26-GCC-4.9.2, UDUNITS/2.2.26-GCC-6.2.0, UDUNITS/2.2.26-intel-2016.u3, ... UDUNITS supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of units, and conversion of values between compatible scales of measurement. - Homepage: http://www.unidata.ucar.edu/software/udunits/ UFL: UFL/1.6.0-intel-2016.u3-Python-2.7.9, UFL/1.6.0-intel-2016.u3-Python-2.7.11, UFL/2016.1.0-intel-2016.u3-Python-2.7.11, ... The Unified Form Language (UFL) is a domain specific language for declaration of finite element discretizations of variational forms. More precisely, it defines a flexible interface for choosing finite element spaces and defining expressions for weak forms in a notation close to mathematical notation. - Homepage: https://launchpad.net/ufl Unblur: Unblur/1.0.2 Unblur is used to align the frames of movies recorded on an electron microscope to reduce image blurring due to beam-induced motion. - Homepage: http://grigoriefflab.janelia.org/unblur VCFtools: VCFtools/0.1.12-GCC-4.9.2-Perl-5.20.0, VCFtools/0.1.12-intel-2016.u3-Perl-5.20.0, VCFtools/0.1.15-foss-2017b-Perl-5.24.1, ... VEP: VEP/94.5-foss-2017b-Perl-5.26.0, VEP/97-foss-2017b-Perl-5.26.0 Variant Effect Predictor (VEP) determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. VMD: VMD/1.9.1, VMD/1.9.3 VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VTK: VTK/6.3.0-intel-2016.u3-test, VTK/6.3.0-intel-2016.u3-Python-2.7.9, VTK/6.3.0-intel-2016.u3-Python-2.7.11, ... VXL: VXL/2.0.2-spartan_gcc-6.2.0 VXL (the Vision-something-Libraries) is a collection of C++ libraries designed for computer vision research and implementation. It was created from TargetJr and the IUE with the aim of making a light, fast and consistent system. VXL is written in ANSI/ISO C++ and is designed to be portable over many platforms. Valgrind: Valgrind/3.9.0-GCC-4.9.2, Valgrind/3.10.0-GCC-4.9.2, Valgrind/3.11.0-GCC-4.9.2, Valgrind/3.12.0-GCC-4.9.2, ... Valgrind: Debugging and profiling tools - Homepage: http://valgrind.org/downloads/ Velvet: Velvet/1.2.10-GCC-4.9.2-mt-kmer_57, Velvet/1.2.10-intel-2016.u3-mt-kmer_57, Velvet/1.2.10-intel-2017.u2-mt-kmer_57, ... VelvetOptimiser: VelvetOptimiser/2.2.5-intel-2017.u2-mt-kmer_191, VelvetOptimiser/2.2.5-intel-2017.u2 VelvetOptimiser is a multi-threaded Perl script for automatically optimising the three primary parameter options (K, -exp_cov, -cov_cutoff) for the Velvet de novo sequence assembler. ViennaRNA: ViennaRNA/2.1.3-GCC-4.9.2, ViennaRNA/2.1.3-GCC-4.9.3 Software and Documents from the Theoretical Biochemistry Institute, University of Vienna Voro++: Voro++/0.4.6-GCC-6.2.0, Voro++/0.4.6-intel-2017.u2-GCC-6.2.0-CUDA9 Voro++ is a software library for carrying out three-dimensional computations of the Voronoi tessellation. A distinguishing feature of the Voro++ library is that it carries out cell-based calculations, computing the Voronoi cell for each particle individually. It is particularly well-suited for applications that rely on cell-based statistics, where features of Voronoi cells (eg. volume, centroid, number of faces) can be used to analyze a system of particles. Vt: Vt/0.5772-spartan_gcc-6.2.0 vt is a variant tool set that discovers short variants from Next Generation Sequencing data. WRF: WRF/3.6.1-intel-2016.u3-dmpar The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs. - Homepage: http://www.wrf-model.org Wine: Wine/1.8.6, Wine/4.0.0-GCC-6.2.0 Wine: Free implementation of Windows on Unix - Homepage: http://www.winehq.com/ X11: X11/20160819-foss-2017b, X11/20160819-GCC-4.9.2, X11/20160819-GCC-6.2.0, X11/20160819-intel-2016.u3, X11/20160819-intel-2017.u2, ... The X Window System (X11) is a windowing system for bitmap displays X11-Applications: X11-Applications/20160819-intel-2016.u3 The X Window System (X11) is a windowing system for bitmap displays XKeyboardConfig: XKeyboardConfig/2.16-intel-2016.u3-Python-2.7.11, XKeyboardConfig/2.16-intel-2016.u3, ... The non-arch keyboard configuration database for X Window. The goal is to provide the consistent, well-structured, frequently released open source of X keyboard configuration data for X Window System implementations (free, open source and commercial). The project is targeted to XKB-based systems. - Homepage: http://www.freedesktop.org/wiki/Software/XKeyboardConfig/ XML-LibXML: XML-LibXML/2.0132-foss-2017b-Perl-5.26.0, XML-LibXML/2.0132-spartan_intel-2017.u2-Perl-5.26.0 Perl binding for libxml2 XML-Parser: XML-Parser/2.41-foss-2017b-Perl-5.24.1, XML-Parser/2.41-GCC-4.9.2-Perl-5.20.0, XML-Parser/2.41-GCC-6.2.0-Perl-5.20.3, ... This is a Perl extension interface to James Clark's XML parser, expat. XML-Writer: XML-Writer/0.625-intel-2016.u3-Perl-5.20.0 Perl extension for writing XML documents. XOP: XOP/2.4 XOP provides a set of codes from different authors and written in different computer languages for modeling of x-ray radiation sources and their interaction with x-ray optical components such as mirrors, filters, and multilayers and offers a variety of analyses and data visualizations. XSD: XSD/4.0.0-intel-2016.u3 CodeSynthesis XSD is an open-source, cross-platform W3C XML Schema to C++ data binding compiler. Provided with an XML instance specification (XML Schema), it generates C++ classes that represent the given vocabulary as well as XML parsing and serialization code. XZ: XZ/5.2.2-foss-2017b, XZ/5.2.2-GCC-4.6.4, XZ/5.2.2-GCC-4.9.2, XZ/5.2.2-GCC-5.4.0, XZ/5.2.2-GCC-6.2.0, XZ/5.2.2-GCC-6.4.0, ... xz: XZ utilities - Homepage: http://tukaani.org/xz/ Xerces-C++: Xerces-C++/3.1.1-GCC-4.9.2, Xerces-C++/3.1.1-GCC-6.2.0, Xerces-C++/3.1.1-intel-2016.u3 Xerces-C++ is a validating XML parser written in a portable subset of C++. Xerces-C++ makes it easy to give your application the ability to read and write XML data. A shared library is provided for parsing, generating, manipulating, and validating XML documents using the DOM, SAX, and SAX2 APIs. - Homepage: http://xerces.apache.org/xerces-c/ Xpress: Xpress/Xpress-7.9 FICO Xpress is the premier mathematical modeling and optimization software suite - Homepage: http://www.fico.com/en/products/fico-xpress-optimization Yambo: Yambo/3.4.2-intel-2016.u3 Yambo is a FORTRAN/C code for Many-Body calculations in solid state and molecular physics. Yambo relies on the Kohn-Sham wavefunctions generated by two DFT public codes: abinit, and PWscf. - Homepage: http://www.yambo-code.org Yasm: Yasm/1.3.0-GCC-4.9.2, Yasm/1.3.0-GCC-6.2.0, Yasm/1.3.0-intel-2016.u3, Yasm/1.3.0-intel-2017.u2-GCC-5.4.0-CUDA8, ... Yasm: Complete rewrite of the NASM assembler with BSD license ZeroMQ: ZeroMQ/3.2.5-intel-2016.u3, ZeroMQ/4.2.5-intel-2016.u3, ZeroMQ/4.2.5-spartan_intel-2017.u2 ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. It gives you sockets that carry atomic messages across various transports like in-process, inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous message-processing tasks. It has a score of language APIs and runs on most operating systems. - Homepage: http://www.zeromq.org/ abacas: abacas/1.3.1 ant: ant/1.10.0-Java-1.8.0_71, ant/1.10.1-Java-1.8.0_152, ant/1.10.2-Java-9.0.4 Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications. - Homepage: http://ant.apache.org/ apex: apex/0.1a-intel-2017.u2-Python-3.6.4, apex/0.1-intel-2017.u2-Python-3.6.4 This repository holds NVIDIA-maintained utilities to streamline mixed precision and distributed training in Pytorch. Some of the code here will be included in upstream Pytorch eventually. The intention of Apex is to make up-to-date utilities available to users as quickly as possible. armatus: armatus/2.3-intel-2017.u2 Multiresolution domain calling software for chromosome conformation capture interaction matrices. arpack-ng: arpack-ng/3.3.0-intel-2016.u3, arpack-ng/3.3.0-iompi-2016.u3, arpack-ng/3.5.0-intel-2016.u3, ... ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. - Homepage: http://forge.scilab.org/index.php/p/arpack-ng/ at-spi2-atk: at-spi2-atk/2.30.0-intel-2017.u2 GTK+ module for bridging AT-SPI to ATK at-spi2-core: at-spi2-core/2.30.0-intel-2017.u2, at-spi2-core/2.30.0-intel-2018.u4 GTK+ module for bridging AT-SPI to ATK awscli: awscli/1.16.67-GCC-6.2.0 Universal Command Line Interface for Amazon Web Services azcopy: azcopy/7.3.0 bcalm: bcalm/2.2.3 BCALM 2 is a bioinformatics tool for constructing the compacted de Bruijn graph from sequencing data. bcl2fastq2: bcl2fastq2/2-20-0 bdw-gc: bdw-gc/8.0.4-GCC-6.2.0, bdw-gc/8.0.4-intel-2017.u2 The Boehm-Demers-Weiser conservative garbage collector can be used as a garbage collecting replacement for C malloc or C++ new. It allows you to allocate memory basically as you normally would, without explicitly deallocating memory that is no longer useful. The collector automatically recycles memory when it determines that it can no longer be otherwise accessed. beagle-lib: beagle-lib/2.1.2-GCC-4.9.2, beagle-lib/2.1.2-goolf-2015a, beagle-lib/2.1.2-intel-2016.u3, ... berokka: berokka/0.2.3-spartan_intel-2017.u2 Trim, circularise and orient long read bacterial genome assemblies binutils: binutils/2.25-foss-2017b-binutils-2.25, binutils/2.25-foss-2017b, binutils/2.25-GCC-4.9.2-binutils-2.25, ... binutils: GNU binary utilities - Homepage: http://directory.fsf.org/project/binutils/ biobambam: biobambam/0.0.99-intel-2016.u3 blasr: blasr/smrtanalysis-2.1-GCC-4.9.2 BLASR (Basic Local Alignment with Successive Refinement) rapidly maps reads to genomes by finding the highest scoring local alignment or set of local alignments between the read and the genome. Optimized for PacBio's extraordinarily long reads and taking advantage of rich quality values, BLASR maps reads rapidly with high accuracy. blobtools: blobtools/0.9.19.4-intel-2016.u3 Blobtools is a tool set for the visualisation of (draft) genome assemblies using TAGC (Taxon-annotated Gc-Coverage) plots Kumar et al. 2012. bloocoo: bloocoo/1.0.7 Bloocoo is a k-mer spectrum-based read error corrector, designed to correct large datasets with a very low memory footprint. bmtools: bmtools/20140221-intel-2017.u2 bmtools is part of BMTagger aka Best Match Tagger, for removing human reads from metagenomics datasets. bmvdgeijn-WASP: bmvdgeijn-WASP/0.3.3-intel-2017.u2-Python-3.6.4 WASP is a suite of tools for unbiased allele-specific read mapping and discovery of molecular QTLs. botocore: botocore/1.12.58-GCC-6.2.0 Universal Command Line Interface for Amazon Web Services bzip2: bzip2/1.0.6-foss-2017b, bzip2/1.0.6-GCC-4.9.2, bzip2/1.0.6-GCC-4.9.3, bzip2/1.0.6-GCC-5.4.0, bzip2/1.0.6-GCC-6.2.0-noavx2, ... cMESS: cMESS/1.0.0-spartan_intel-2017.u2-Python-2.7.13 M.E.S.S. is the successor to the LyaPack Toolbox for MATLAB. It is intended for solving large sparse matrix equations. cURL: cURL/7.43.0-GCC-4.9.2, cURL/7.43.0-GCC-5.4.0, cURL/7.43.0-intel-2016.u3, cURL/7.43.0-intel-2017.u2-GCC-6.2.0-CUDA9.1, ... cairo: cairo/1.12.18-GCC-4.9.2, cairo/1.12.18-intel-2016.u3, cairo/1.14.6-GCC-4.9.2, cairo/1.14.6-goolf-2015a, ... capnproto: capnproto/0.5.3-GCC-4.9.2 The Cap’n Proto tools, including the compiler (which takes .capnp files and generates source code for them), are written in C++. Therefore, you must install the C++ package even if your actual development language is something else. cddlib: cddlib/0.94-GCC-4.9.2 The C-library cddlib is a C implementation of the Double Description Method of Motzkin et al. centrifuge: centrifuge/1.0.3b-intel-2016.u3, centrifuge/1.0.3b-spartan_intel-2017.u2, centrifuge/1.0.3-intel-2016.u3 [Centrifuge] is a novel microbial classification engine that enables rapid, accurate and sensitive labeling of reads and quantification of species on desktop computers. clustalw: clustalw/2.1-intel-2016.u3, clustalw/2.1-intel-2017.u2 Multiple alignment of nucleic acid and protein sequences concoct: concoct/0.4.0-intel-2017.u2-Python-2.7.11 The Cython language makes writing C extensions for the Python language as easy as Python itself. Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations. cosi2: cosi2/2.02-GCC-4.9.2, cosi2/2.3.0rc4-GCC-4.9.2 cosi2 is an efficient coalescent simulator with support for selection, population structure, variable recombination rates, and gene conversion. It supports exact and approximate simulation modes. cromwell: cromwell/31-Java-1.8.0_71 Cromwell is a Workflow Management System geared towards scientific workflows. cuDNN: cuDNN/5.1-CUDA-8.0.44, cuDNN/5.1-intel-2017.u2-CUDA-8.0.44, cuDNN/5.1-intel-2017.u2-GCC-5.4.0-CUDA8-CUDA-8.0.44, ... The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks. - Homepage: https://developer.nvidia.com/cudnn cub: cub/1.6.4 NVLabs CUB provides state-of-the-art, reusable software components for every layer of the CUDA programming model - Homepage: https://nvlabs.github.io/cub/ cutadapt: cutadapt/1.13-intel-2016.u3-Python-2.7.12, cutadapt/1.13-intel-2016.u3-Python-3.5.2, ... cutadapt removes adapter sequences from high-throughput sequencing data. This is usually necessary when the read length of the sequencing machine is longer than the molecule that is sequenced, for example when sequencing microRNAs. dDocent: dDocent/2.7.6-intel-2017.u2 This script serves as an interactive bash wrapper to QC, assemble, map, and call SNPs from almost any kind of RAD data. dask: dask/0.17.2-intel-2017.u2-Python-3.6.4 Dask provides multi-core execution on larger-than-memory datasets using blocked algorithms and task scheduling. datamash: datamash/1.4-GCC-8.2.0, datamash/1.4-spartan_intel-2017.u2, datamash/1.5-GCC-8.2.0, datamash/1.5-spartan_intel-2017.u2 GNU datamash is a command-line program which performs basic numeric, textual and statistical operations on input textual data files. dbus-glib: dbus-glib/0.106-GCC-6.2.0, dbus-glib/0.108-intel-2016.u3, dbus-glib/0.108-intel-2017.u2 D-Bus is a message bus system, a simple way for applications to talk to one another. dcmtk: dcmtk/3.6.4-spartan_gcc-6.2.0 DCMTK is a collection of libraries and applications implementing large parts the DICOM standard. It includes software for examining, constructing and converting DICOM image files, handling offline media, sending and receiving images over a network connection, as well as demonstrative image storage and worklist servers. deepTools: deepTools/3.1.2-intel-2017.u2-Python-3.6.4 deepTools is a suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq. diamond: diamond/0.9.10 DIAMOND is a sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000. docopt.cpp: docopt.cpp/0.6.2-GCC-6.2.0 docopt.cpp creates beautiful command-line interfaces. dotnetcore-runtime: dotnetcore-runtime/2.2.4-GCCcore-6.4.0 .NET is a free, cross-platform, open source developer platform for building many different types of applications. dotnetcore-sdk: dotnetcore-sdk/2.2.4-GCC-6.2.0, dotnetcore-sdk/2.2.4-GCCcore-6.4.0 .NET is a free, cross-platform, open source developer platform for building many different types of applications. drm_tools: drm_tools/1.1.31-GCC-6.2.0 A collection of small utilities for: data extraction (text or binary files), data buffering, message queue control, column addition, date/time manipulation, and data recovery testing. dsk: dsk/2.2.0-GCC-4.9.2, dsk/2.2.0-GCC-4.9.3 DSK is a k-mer counter for reads or genomes. duck: duck/6.8.3.29107 duck is a WebDAV client. dx-toolkit: dx-toolkit/0.168.0-Python-2.7.9 The DNAnexus Platform SDK (a.k.a. dx-toolkit) includes the dx command-line client, tools for building and debugging apps, and other utilities for working with DNA data on the platform. ea-utils: ea-utils/r805-GCC-4.8.1, ea-utils/r805-GCC-4.9.2, ea-utils/1.1.2-537-GCC-4.9.2, ea-utils/1.04.807-GCC-4.9.2, ... Command-line tools for processing biological sequencing data. Barcode demultiplexing, adapter trimming, etc. Primarily written to support an Illumina based pipeline - but should work with any FASTQs. easyspin: easyspin/5.2.21-intel-2017.u2, easyspin/5.2.21 EasySpin is a MATLAB toolbox for simulating and fitting a wide range of Electron Paramagnetic Resonance (EPR) spectra. It supplements the numerical and visualization power of MATLAB with the best computational methods devised by EPR spectroscopists. elastix: elastix/4.9.0-spartan_gcc-6.2.0 elastix: a toolbox for rigid and nonrigid registration of images. emm-typing-tool: emm-typing-tool/Feb012017-GCC-4.9.2 The emm gene typing tool assigns emm type and subtype by querying the CDC M-type specific database (ftp://ftp.cdc.gov/pub/infectious_diseases/biotech/tsemm/) emmtyper: emmtyper/0.1.0-intel-2017.u2-Python-3.6.4 emm Automatic Isolate Labeller eudev: eudev/3.1.2-GCC-4.9.2, eudev/3.1.2-goolf-2015a, eudev/3.1.2-intel-2016.u3, eudev/3.1.2-iomkl-2016.u3 eudev is a fork of systemd-udev with the goal of obtaining better compatibility with existing software such as OpenRC and Upstart, older kernels, various toolchains and anything else required by users and various distributions. - Homepage: https://wiki.gentoo.org/wiki/Project:Eudev exiv2: exiv2/0.27.2-GCC-6.2.0 Exiv2 is a C++ library and a command line utility to read, write, delete and modify Exif, IPTC, XMP and ICC image metadata. exo: exo/0.10.3-intel-2016.u3 - Homepage: https://xfce.org/ expat: expat/2.1.0-foss-2017b, expat/2.1.0-GCC-4.9.2, expat/2.1.0-GCC-6.2.0, expat/2.1.0-GCC-6.4.0, expat/2.1.0-GCCcore-6.4.0, ... faiss: faiss/1.4.0-intel-2017.u2-GCC-6.2.0-CUDA9, faiss/1.4.0-intel-2017.u2 Faiss is a library for efficient similarity search and clustering of dense vectors. It is developed by Facebook AI Research. fastGEAR: fastGEAR/16Dec2016, fastGEAR/20161216 fastStructure: fastStructure/1.0-spartan_intel-2017.u2-Python-2.7.13 A variational framework for inferring population structure from SNP genotype data. fastp: fastp/0.19.7-intel-2017.u2, fastp/0.20.0-intel-2017.u2 A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. fastqc: fastqc/0.11.3, fastqc/0.11.5, fastqc/0.11.8 file: file/5.35-GCC-6.2.0, file/5.35-spartan_intel-2017.u2 The file command is 'a file type guesser', that is, a command-line tool that tells you in words what kind of data a file contains. fixesproto: fixesproto/5.0-GCC-4.9.2, fixesproto/5.0-goolf-2015a, fixesproto/5.0-intel-2016.u3, fixesproto/5.0-intel-2017.u2, ... X.org FixesProto protocol headers. - Homepage: http://www.freedesktop.org/wiki/Software/xlibs flex: flex/2.5.35-GCC-4.9.2, flex/2.5.35-intel-2016.u3, flex/2.5.35-iompi-2016.u3, flex/2.5.39-foss-2017b, ... Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text. foam-extend: foam-extend/4.0-spartan_intel-2017.u2 The foam-extend project is a fork of the OpenFOAM® open source library for Computational Fluid Dynamics (CFD). It is an open project welcoming and integrating contributions from all users and developers. Previously known as OpenFOAM-dev and OpenFOAM-extend, it contains bug fixes and performance improvements, as well as extensions and additional features provided by community contributors (see file ListOfContributors), such as dynamic mesh and topological change support, turbomachinery extensions including general grid interpolation (GGI), cyclic GGI and mixing plane, block-coupled matrix support, implicitly coupled conjugate heat transfer and other physics coupling, finite area method, comprehensive dynamic mesh (motion and topological changes) capability and GPU support. fontconfig: fontconfig/2.11.1-GCC-4.9.2, fontconfig/2.11.1-goolf-2015a, fontconfig/2.11.1-intel-2016.u3, ... fontsproto: fontsproto/2.1.3-GCC-4.9.2, fontsproto/2.1.3-goolf-2015a, fontsproto/2.1.3-intel-2016.u3, fontsproto/2.1.3-iomkl-2016.u3 X11 font extension wire protocol - Homepage: http://www.freedesktop.org/wiki/Software/xlibs foss: foss/2017b GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK. fpc: fpc/3.0.4 fpc: Free Pascal is a professional Pascal compiler. freebayes: freebayes/1.2.0-foss-2017b, freebayes/1.2.0-intel-2017.u2 Bayesian haplotype-based polymorphism discovery and genotyping. freeglut: freeglut/2.8.1-goolf-2015a, freeglut/2.8.1-intel-2016.u3, freeglut/3.0.0-intel-2016.u3, freeglut/3.0.0-intel-2017.u2, ... freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library. - Homepage: http://freeglut.sourceforge.net/ freetype: freetype/2.5.3-GCC-4.9.2, freetype/2.5.5-foss-2017b, freetype/2.5.5-GCC-4.9.2, freetype/2.5.5-GCC-6.4.0, ... FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display servers, font conversion tools, text image generation tools, and many other products as well. fsm-lite: fsm-lite/1.0-spartan_intel-2017.u2 A singe-core implemetation of frequency-based substring mining. future: future/0.16.0-spartan_intel-2017.u2-Python-2.7.13 This library is the reference implementation of the Python wheel packaging standard, as defined in PEP 427. fxtract: fxtract/2.3-GCC-4.9.4 Extract sequences from a fastx (fasta or fastq) file given a subsequence. g2clib: g2clib/1.6.0-intel-2017.u2, g2clib/1.6.0-spartan_intel-2017.u2 Library contains GRIB2 encoder/decoder ('C' version). g2lib: g2lib/1.4.0-spartan_intel-2017.u2 Library contains GRIB2 encoder/decoder and search/indexing routines. garcon: garcon/0.4.0-intel-2016.u3 - Homepage: https://xfce.org/ gatb-core: gatb-core/1.1.0, gatb-core/1.2.1, gatb-core/1.3.0 Genome Analysis Toolbox with de-Bruijn graph gcccuda: gcccuda/2017.01 GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit. gdrcopy: gdrcopy/2.0-GCC-6.2.0, gdrcopy/2.0-GCC-6.4.0-2.28, gdrcopy/2.0-GCCcore-8.3.0 A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology. gettext: gettext/0.19.2-foss-2017b, gettext/0.19.2-GCC-4.6.4, gettext/0.19.2-GCC-4.9.2, gettext/0.19.2-GCC-5.4.0, ... GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation - Homepage: http://www.gnu.org/software/gettext/ gflags: gflags/2.1.2-GCC-4.9.2, gflags/2.1.2-intel-2016.u3, gflags/2.1.2-intel-2017.u2-GCC-5.4.0-CUDA8, gflags/2.2.1-intel-2017.u2 gfootball: gfootball/0.2-intel-2017.u2-GCC-6.2.0-CUDA9-Python-3.6.4 This repository contains a RL environment based on open-source game Gameplay Football. It was created by Google Brain team for research purposes. git: git/1.8.5.6-GCC-4.9.2, git/2.10.0-GCC-4.9.2, git/2.19.1-GCC-6.2.0, git/2.19.1-intel-2017.u2 glew: glew/2.1.0-spartan_gcc-8.1.0 The OpenGL Extension Wrangler Library The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source C/C++ extension loading library. GLEW provides efficient run-time mechanisms for determining which OpenGL extensions are supported on the target platform. OpenGL core and extension functionality is exposed in a single header file. GLEW has been tested on a variety of operating systems, including Windows, Linux, Mac OS X, FreeBSD, Irix, and Solaris. glibc: glibc/2.26-GCCcore-6.4.0 The GNU C Library project provides the core libraries for the GNU system and GNU/Linux systems, as well as many other systems that use Linux as the kernel. glibmm: glibmm/2.46.1-intel-2017.u2-GCC-6.2.0-CUDA9, glibmm/2.46.1-intel-2017.u2, glibmm/2.46.1-spartan_intel-2017.u2, ... This is glibmm, a C++ API for parts of glib that are useful for C++. glog: glog/0.3.4-GCC-4.9.2, glog/0.3.4-intel-2016.u3, glog/0.3.4-intel-2017.u2-GCC-5.4.0-CUDA8, glog/0.3.4, glog/0.3.5-intel-2017.u2 glproto: glproto/1.4.16-GCC-4.9.2, glproto/1.4.16-goolf-2015a, glproto/1.4.16-intel-2016.u3, glproto/1.4.16-iomkl-2016.u3 glxgears: glxgears/0.1-spartan_gcc-8.1.0 gmsh: gmsh/3.0.6 gmsh is a 3D finite element mesh generator with a build-in CAD engine and post-processor. gmvapich2: gmvapich2/2.3.2, gmvapich2/2016a GNU Compiler Collection (GCC) based compiler toolchain, including MVAPICH2 for MPI support. gnucobol: gnucobol/3.0-rc1-GCC-4.9.2, gnucobol/3.0-rc1-GCC-6.2.0 GnuCOBOL (formerly OpenCOBOL) is a free COBOL compiler. cobc translates COBOL source to executable using intermediate C, designated C compiler and linker. gnuplot: gnuplot/5.0.0-foss-2017b, gnuplot/5.0.0-GCC-4.9.2, gnuplot/5.0.0-GCC-6.2.0, gnuplot/5.0.0-intel-2017.u2 gompi: gompi/GCC-4.6.4-OpenMPI-1.8.4, gompi/GCC-6.2.0-OpenMPI-3.0.0, gompi/2015a, gompi/2016b, gompi/2017a, gompi/2017b, ... gompic: gompic/2017.01 GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, including OpenMPI for MPI support with CUDA features enabled. goolf: goolf/2015a goolfc: goolfc/2017.01 GCC based compiler toolchain __with CUDA support__, and including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK. gperf: gperf/3.0.4-foss-2017b, gperf/3.0.4-GCC-4.9.2, gperf/3.0.4-GCC-6.2.0, gperf/3.0.4-GCC-6.4.0, gperf/3.0.4-GCCcore-6.4.0, ... GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single string comparison only. - Homepage: http://www.gnu.org/software/gperf/ grace: grace/5.1.25-intel-2016.u3 Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif. - Homepage: http://freecode.com/projects/grace gretl: gretl/2018c-GCC-6.2.0-LAPACK-3.8.0-OpenBLAS-0.3.5 A cross-platform software package for econometric analysis. gtk-xfce-engine: gtk-xfce-engine/2.10.0-intel-2016.u3 - Homepage: http:/xfce.org/ guile: guile/2.0.14.16-GCC-6.2.0 Guile is designed to help programmers create flexible applications that can be extended by users or other programmers with plug-ins, modules, or scripts. gzip: gzip/1.8-goolf-2015a gzip (GNU zip) is a popular data compression program as a replacement for compress gzstream: gzstream/1.5-GCC-4.9.2, gzstream/1.5-intel-2016.u3 Gzstream is a small C++ library, basically just a wrapper, that provides the functionality of the zlib C-library in a C++ iostream. h2o4gpu: h2o4gpu/0.2.0-intel-2017.u2-GCC-6.2.0-CUDA9-Python-3.6.4-GPU An open-source software library for Machine Intelligence h5py: h5py/2.7.1-intel-2017.u2-Python-2.7.13 HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data. hdbscan: hdbscan/0.8.18-intel-2017.u2-Python-3.6.4 Hierarchical Density-Based Spatial Clustering of Applications with Noise. Performs DBSCAN over varying epsilon values and integrates the result to find a clustering that gives the best stability over epsilon. This allows HDBSCAN to find clusters of varying densities (unlike DBSCAN), and be more robust to parameter selection. help2man: help2man/1.47.4-foss-2017b, help2man/1.47.4-GCCcore-6.3.0, help2man/1.47.4-GCCcore-6.4.0, help2man/1.47.4-GCCcore-7.3.0, ... help2man produces simple manual pages from the '--help' and '--version' output of other commands. hwloc: hwloc/1.10.0-GCC-4.9.2, hwloc/1.10.1-GCC-4.6.4, hwloc/1.10.1-GCC-4.9.2, hwloc/1.10.1-GCC-6.2.0, hwloc/1.10.1-intel-2016.u3, ... The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently. iCP: iCP/1.4 interface Comsol PhreeqC icc: icc/2016.u3-GCC-4.9.2, icc/2017.u2-GCC-5.4.0, icc/2017.u2-GCC-6.2.0, icc/2018.u4-GCC-8.2.0, icc/2019.4.243-GCC-8.3.0-2.32 iccifort: iccifort/2016.u3-GCC-4.9.2, iccifort/2017.u2-GCC-5.4.0, iccifort/2017.u2-GCC-6.2.0, iccifort/2018.u4-GCC-8.2.0, ... iccifortcuda: iccifortcuda/2018.u4-GCC-8.2.0 Intel C, C++ & Fortran compilers with CUDA toolkit iceauth: iceauth/1.0.5-intel-2016.u3 - Homepage: http://www.x.org idemp: idemp/07062017-spartan_gcc-6.2.0 idemp work needs to be done: trim R1 reads to get rid of barcodes in case R1 reads into barcode when template is short. ifort: ifort/2016.u3-GCC-4.9.2, ifort/2017.u2-GCC-5.4.0, ifort/2017.u2-GCC-6.2.0, ifort/2018.u4-GCC-8.2.0, ... iimpi: iimpi/2016.u3-GCC-4.9.2, iimpi/2017.u2-GCC-5.4.0, iimpi/2017.u2-GCC-6.2.0, iimpi/2018.u4-GCC-8.2.0, iimpi/2019.u4 Intel C/C++ and Fortran compilers, alongside Intel MPI. imake: imake/1.0.5-goolf-2015a imake is a Makefile-generator that is intended to make it easier to develop software portably for multiple systems. - Homepage: http://www.x.org/ imkl: imkl/11.3.3.210-iimpi-2016.u3-GCC-4.9.2, imkl/11.3.3.210-iompi-2016.u3, imkl/2017.2.174-iimpi-2017.u2-GCC-5.4.0, ... Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more. impi: impi/5.1.3.223-iccifort-2016.u3-GCC-4.9.2, impi/2017.2.174-iccifort-2017.u2-GCC-5.4.0, ... The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification. inputproto: inputproto/2.3.1-foss-2017b, inputproto/2.3.1-GCC-4.9.2, inputproto/2.3.1-GCC-6.2.0, inputproto/2.3.1-goolf-2015a, ... X.org InputProto protocol headers. - Homepage: http://www.freedesktop.org/wiki/Software/xlibs intel: intel/2016.u3-GCC-4.9.2-CUDA7.5, intel/2016.u3, intel/2017.u2-CUDA8, intel/2017.u2-GCC-5.4.0-CUDA8, ... Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL. intltool: intltool/0.51.0-foss-2017b, intltool/0.51.0-GCC-4.9.2, intltool/0.51.0-GCC-6.2.0-Perl-5.20.3, intltool/0.51.0-GCC-6.2.0, ... intltool is a set of tools to centralize translation of many different file formats using GNU gettext-compatible PO files. iomkl: iomkl/2016.u3 Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI. - Homepage: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/ iomklc: iomklc/2018.u4 Intel Cluster Toolchain Compiler Edition Intel C/C++ and Fortran compilers, Intel MKL, plus nVidia CUDA. With added OpenMPI, ucx tuned for Spartan's gpgpu cluster. iompi: iompi/spartan_intel, iompi/2016.u3, iompi/2017.u2-cuda9.1, iompi/2017.u2 Toolchain with Intel C, C++ and Fortran compilers, alongside OpenMPI. - Homepage: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/ iompic: iompic/2018.u4 Intel C/C++ and Fortran compilers, alongside Open MPI. iqtree: iqtree/1.4.2, iqtree/1.5.0a, iqtree/1.5.1-intel-2016.u3, iqtree/1.6.7-intel-2016.u3, iqtree/1.6.7-intel-2017.u2-nompi, ... Efficient phylogenomic software by maximum likelihood isPcr: isPcr/33-intel-2017.u2, isPcr/33-spartan_intel-2017.u2 Command line program that builds its own index (rather than relying on gfServer) to do PCR. jemalloc: jemalloc/5.0.1-foss-2017b, jemalloc/5.0.1-GCC-6.4.0, jemalloc/5.0.1-GCCcore-6.4.0, jemalloc/5.0.1-intel-2016.u3 jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and scalable concurrency support. jintest1: jintest1/1.2.11-GCCcore-8.3.0 zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system. joe: joe/4.6 JOE is a full featured terminal-based screen editor. jsonschema: jsonschema/2.6.0-intel-2017.u2-Python-3.6.4 Python plotting library for collaborative, interactive, publication-quality graphs. jupyter: jupyter/1.0.0-GCC-6.2.0-Python-2.7.13, jupyter/1.0.0-GCC-6.2.0-Python-3.7.1, jupyter/1.0.0-spartan_gcc-6.2.0-Python-3.7.3 The Jupyter Notebook is an open-source web application that allows you to create and share documents that contain live code, equations, visualizations and narrative text. Uses include: data cleaning and transformation, numerical simulation, statistical modeling, data visualization, machine learning, and much more. kWIP: kWIP/0.2.0-intel-2016.u3 The k-mer Weighted Inner Product. kbproto: kbproto/1.0.6-GCC-4.9.2, kbproto/1.0.6-GCC-6.2.0, kbproto/1.0.6-intel-2016.u3, kbproto/1.0.6-intel-2017.u2, ... X.org KBProto protocol headers. - Homepage: http://www.freedesktop.org/wiki/Software/xlibs kentUtils: kentUtils/302.1.0-GCC-4.9.2 khmer: khmer/2.0-intel-2016.u3-Python-2.7.10 The khmer software is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. lasagne: lasagne/v0.2-dev-intel-2017.u2-GCC-6.2.0-CUDA9-Python-3.5.2-Tensorflow-1.10.0, ... Lasagne is a lightweight library to build and train neural networks in Theano leon: leon/1.0.0 Leon is a software to compress Next Generation Sequencing data. It can compress Fasta or Fastq format; plain text and gzipped files are supported. leveldb: leveldb/1.19-GCC-4.9.2, leveldb/1.19-intel-2016.u3, leveldb/1.19-intel-2017.u2-GCC-5.4.0-CUDA8 LevelDB is a fast key-value storage library written at Google that provides an ordered mapping from string keys to string values. - Homepage: https://github.com/google/leveldb/ libGLU: libGLU/9.0.0-foss-2017b, libGLU/9.0.0-GCC-4.9.2, libGLU/9.0.0-GCC-6.2.0-Mesa-17.2.8, libGLU/9.0.0-GCC-6.2.0, ... The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. - Homepage: ftp://ftp.freedesktop.org/pub/mesa/glu/ libICE: libICE/1.0.9-GCC-6.2.0, libICE/1.0.9-goolf-2015a, libICE/1.0.9-intel-2016.u3, libICE/1.0.9-intel-2017.u2, ... X Inter-Client Exchange library for freedesktop.org libSM: libSM/1.2.2-GCC-6.2.0, libSM/1.2.2-goolf-2015a, libSM/1.2.2-intel-2016.u3, libSM/1.2.2-intel-2017.u2, ... X11 Session Management library, which allows for applications to both manage sessions, and make use of session managers to save and restore their state for later use. libX11: libX11/1.6.3-foss-2017b-Python-2.7.14, libX11/1.6.3-GCC-4.9.2-Python-2.7.9, libX11/1.6.3-GCC-4.9.2-Python-2.7.11, ... X11 client-side library libXau: libXau/1.0.8-foss-2017b, libXau/1.0.8-GCC-4.9.2, libXau/1.0.8-GCC-6.2.0, libXau/1.0.8-goolf-2015a, libXau/1.0.8-intel-2016.u3, ... The libXau package contains a library implementing the X11 Authorization Protocol. This is useful for restricting client access to the display. - Homepage: http://www.freedesktop.org/wiki/Software/xlibs libXaw: libXaw/1.0.12-goolf-2015a libXaw provides the Athena Widgets toolkit - Homepage: http://www.freedesktop.org/wiki/Software/xlibs libXcursor: libXcursor/1.1.14-intel-2016.u3, libXcursor/1.1.14-intel-2017.u2 X Cursor management library - Homepage: http://www.freedesktop.org/wiki/Software/xlibs libXdamage: libXdamage/1.1.4-GCC-4.9.2, libXdamage/1.1.4-goolf-2015a, libXdamage/1.1.4-intel-2016.u3, libXdamage/1.1.4-iomkl-2016.u3 X Damage extension library - Homepage: http://www.freedesktop.org/wiki/Software/xlibs libXdmcp: libXdmcp/1.1.2-foss-2017b, libXdmcp/1.1.2-GCC-4.9.2, libXdmcp/1.1.2-GCC-6.2.0, libXdmcp/1.1.2-goolf-2015a, ... The libXdmcp package contains a library implementing the X Display Manager Control Protocol. This is useful for allowing clients to interact with the X Display Manager. - Homepage: http://www.freedesktop.org/wiki/Software/xlibs libXext: libXext/1.3.3-GCC-4.9.2, libXext/1.3.3-GCC-6.2.0, libXext/1.3.3-goolf-2015a, libXext/1.3.3-intel-2016.u3-Python-2.7.11, ... Common X Extensions library - Homepage: http://www.freedesktop.org/wiki/Software/xlibs libXfixes: libXfixes/5.0.1-GCC-4.9.2, libXfixes/5.0.1-goolf-2015a, libXfixes/5.0.1-intel-2016.u3, libXfixes/5.0.1-intel-2017.u2, ... X Fixes extension library - Homepage: http://www.freedesktop.org/wiki/Software/xlibs libXfont: libXfont/1.5.1-GCC-4.9.2-Python-2.7.9, libXfont/1.5.1-goolf-2015a-Python-2.7.10, libXfont/1.5.1-intel-2016.u3-Python-2.7.9, ... X font libary - Homepage: http://www.freedesktop.org/wiki/Software/xlibs libXft: libXft/2.3.2-GCC-4.9.2, libXft/2.3.2-GCC-6.2.0-new, libXft/2.3.2-GCC-6.2.0, libXft/2.3.2-intel-2016.u3, ... libXi: libXi/1.7.4-goolf-2015a, libXi/1.7.4-intel-2016.u3-Python-2.7.11, libXi/1.7.4-intel-2016.u3, libXi/1.7.4-intel-2017.u2, ... LibXi provides an X Window System client interface to the XINPUT extension to the X protocol. - Homepage: http://www.freedesktop.org/wiki/Software/xlibs libXinerama: libXinerama/1.1.3-intel-2016.u3, libXinerama/1.1.3-intel-2017.u2 Xinerama multiple monitor library - Homepage: http://www.freedesktop.org/wiki/Software/xlibs libXmu: libXmu/1.1.2-goolf-2015a, libXmu/1.1.2-intel-2016.u3 libXmu provides a set of miscellaneous utility convenience functions for X libraries to use. libXmuu is a lighter-weight version that does not depend on libXt or libXext - Homepage: http://www.freedesktop.org/wiki/Software/xlibs libXp: libXp/1.0.3-intel-2016.u3, libXp/1.0.3-spartan_intel-2017.u2 libXp provides the X print library. - Homepage: http://www.freedesktop.org/wiki/Software/xlibs libXpm: libXpm/3.5.11-goolf-2015a, libXpm/3.5.11-intel-2016.u3, libXpm/3.5.11-intel-2017.u2 libXp provides the X print library. - Homepage: http://www.freedesktop.org/wiki/Software/xlibs libXrandr: libXrandr/1.5.0-intel-2016.u3, libXrandr/1.5.0-intel-2017.u2 X Resize, Rotate and Reflection extension library - Homepage: http://www.freedesktop.org/wiki/Software/xlibs libXrender: libXrender/0.9.9-intel-2016.u3-Python-2.7.9, libXrender/0.9.9-intel-2016.u3-Python-2.7.11, libXrender/0.9.9-intel-2016.u3, ... X11 client-side library - Homepage: http://www.freedesktop.org/wiki/Software/xlibs libXt: libXt/1.1.5-goolf-2015a, libXt/1.1.5-intel-2016.u3-Python-2.7.9, libXt/1.1.5-intel-2016.u3-Python-2.7.11, ... libXt provides the X Toolkit Intrinsics, an abstract widget library upon which other toolkits are based. Xt is the basis for many toolkits, including the Athena widgets (Xaw), and LessTif (a Motif implementation). - Homepage: http://www.freedesktop.org/wiki/Software/xlibs libXtst: libXtst/1.2.2-intel-2017.u2, libXtst/1.2.3-intel-2018.u4 Client library for X Record and Test extensions. libXxf86vm: libXxf86vm/1.1.4-GCC-6.2.0 X11 XFree86 video mode extension library libcanberra: libcanberra/0.30-GCC-6.2.0, libcanberra/0.30-intel-2016.u3, libcanberra/0.30-intel-2017.u2 libccmio: libccmio/2.6.1-spartan_gcc-6.2.0, libccmio/2.6.1-spartan_intel-2017.u2 libdap: libdap/3.19.1-intel-2016.u3, libdap/3.19.1-intel-2017.u2 A C++ SDK which contains an implementation of DAP 2.0 and the development versions of DAP3, up to 3.4. This includes both Client- and Server-side support classes. libdrm: libdrm/2.4.27-GCC-4.9.2, libdrm/2.4.27-intel-2016.u3, libdrm/2.4.64-GCC-4.9.2, libdrm/2.4.64-goolf-2015a, ... libelf: libelf/0.8.13-GCC-4.9.2 libepoxy: libepoxy/1.4.3-intel-2016.u3, libepoxy/1.4.3-intel-2017.u2, libepoxy/1.4.3-intel-2018.u4 Epoxy is a library for handling OpenGL function pointer management for you libexif: libexif/0.6.21-intel-2016.u3 The libexif package contains a library for parsing, editing, and saving EXIF data. Most digital cameras produce EXIF files, which are JPEG files with extra tags that contain information about the image. All EXIF tags described in EXIF standard 2.1 are supported. - Homepage: http://libexif.sourceforge.net/ libffcall: libffcall/1.13-GCC-6.2.0, libffcall/1.13-GCCcore-6.4.0 GNU Libffcall is a collection of four libraries which can be used to build foreign function call interfaces in embedded interpreters libffi: libffi/3.1-intel-2016.u3, libffi/3.1-iomkl-2016.u3, libffi/3.2.1-foss-2017b, libffi/3.2.1-GCC-4.9.2, libffi/3.2.1-GCC-5.4.0, ... The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run-time. - Homepage: http://sourceware.org/libffi/ libfontenc: libfontenc/1.1.3-GCC-4.9.2, libfontenc/1.1.3-goolf-2015a, libfontenc/1.1.3-intel-2016.u3, libfontenc/1.1.3-iomkl-2016.u3 X11 font encoding library - Homepage: http://www.freedesktop.org/wiki/Software/xlibs/ libgd: libgd/2.1.0-GCC-4.9.2, libgd/2.1.0-intel-2016.u3, libgd/2.1.0-intel-2017.u2-GCC-6.2.0-CUDA9, libgd/2.1.0-intel-2017.u2, ... libgeotiff: libgeotiff/1.4.2-spartan_gcc-6.2.0 Library for reading and writing coordinate system information from/to GeoTIFF files libgladeui: libgladeui/3.8.5-intel-2016.u3GTK+2 - Homepage: https://glade.gnome.org libgpuarray: libgpuarray/0.7.6-intel-2017.u2-GCC-6.2.0-CUDA9-Python-3.5.2, libgpuarray/0.7.6-intel-2017.u2-Python-2.7.11-CUDA9, ... Library to manipulate tensors on the GPU. libgtextutils: libgtextutils/0.6.1-intel-2016.u3 libgudev: libgudev/230-intel-2016.u3 libgudev is a library with GObject bindings to libudev - Homepage: https://wiki.gnome.org/Projects/libgudev libharu: libharu/2.2.0-intel-2016.u3, libharu/2.3.0-spartan_intel-2017.u2 libiconv: libiconv/1.15-spartan_gcc-6.2.0 Libiconv converts from one character encoding to another through Unicode conversion libidn: libidn/1.34-GCC-8.2.0, libidn/1.34-intel-2016.u3, libidn/1.34-spartan_gcc-6.2.0, libidn/1.34-spartan_intel-2017.u2 GNU Libidn is a fully documented implementation of the Stringprep, Punycode and IDNA specifications. Libidn's purpose is to encode and decode internationalized domain names. libjpeg: libjpeg/9c-intel-2016.u3 This package contains C software to implement JPEG image encoding, decoding, and transcoding. JPEG is a standardized compression method for full-color and grayscale images. libjpeg-turbo: libjpeg-turbo/1.4.0-foss-2017b, libjpeg-turbo/1.4.0-GCC-4.9.2, libjpeg-turbo/1.4.0-GCC-6.2.0, ... libmatheval: libmatheval/1.1.11-spartan_gcc-6.2.0-cuda9.2 GNU libmatheval is a library (callable from C and Fortran) to parse and evaluate symbolic expressions input as text. libmaus: libmaus/0.0.99-intel-2016.u3 libmaus2: libmaus2/2.0.9-intel-2016.u3 libmng: libmng/2.0.3-intel-2016.u3 libmng -THE reference library for reading, displaying, writing and examining Multiple-Image Network Graphics. MNG is the animation extension to the popular PNG image-format. - Homepage: https://sourceforge.net/projects/libmng/ libogg: libogg/1.3.2-GCC-6.2.0, libogg/1.3.2-intel-2016.u3, libogg/1.3.2-intel-2017.u2 libpciaccess: libpciaccess/0.13.1-foss-2017b, libpciaccess/0.13.1-GCC-4.9.2, libpciaccess/0.13.1-GCC-6.2.0, ... libpng: libpng/1.5.30-intel-2017.u2, libpng/1.6.6-goolf-2015a, libpng/1.6.12-GCC-4.9.2, libpng/1.6.16-intel-2016.u3, ... libpng is the official PNG reference library libpthread-stubs: libpthread-stubs/0.3-foss-2017b, libpthread-stubs/0.3-GCC-4.9.2, libpthread-stubs/0.3-GCC-6.2.0, ... libraw: libraw/0.19.5-intel-2017.u2 LibRaw is a library for reading RAW files from digital cameras libreadline: libreadline/6.3-GCC-4.6.4, libreadline/6.3-GCC-4.9.2, libreadline/6.3-GCC-4.9.3, libreadline/6.3-GCC-5.4.0, ... libsigc++: libsigc++/2.6.1-intel-2017.u2-GCC-6.2.0-CUDA9, libsigc++/2.6.1-intel-2017.u2, libsigc++/2.6.1-spartan_gcc-8.1.0, ... The libsigc++ package implements a typesafe callback system for standard C++. libsigsegv: libsigsegv/2.11-GCC-6.2.0, libsigsegv/2.11-GCCcore-6.4.0, libsigsegv/2.11-intel-2016.u3 GNU libsigsegv is a library for handling page faults in user mode. libsndfile: libsndfile/1.0.28-GCC-6.2.0, libsndfile/1.0.28-intel-2017.u2, libsndfile/1.0.28-intel-2018.u4, ... Libsndfile is a C library for reading and writing files containing sampled sound (such as MS Windows WAV and the Apple/SGI AIFF format) through one standard library interface. libsodium: libsodium/1.0.17-intel-2016.u3, libsodium/1.0.17-spartan_intel-2017.u2 Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more. libtool: libtool/2.4.5-GCC-4.9.2, libtool/2.4.6-foss-2017b, libtool/2.4.6-GCC-4.6.4, libtool/2.4.6-GCC-4.9.2, libtool/2.4.6-GCC-5.4.0, ... GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface. libunistring: libunistring/0.9.10-GCC-6.2.0 This library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard. libunwind: libunwind/1.1-goolf-2015a, libunwind/1.2.1-GCC-6.2.0, libunwind/1.2.1-GCCcore-6.4.0, libunwind/1.3.1-spartan_gcc-8.1.0 The primary goal of libunwind is to define a portable and efficient C programming interface (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain (non-local goto). The API supports both local (same-process) and remote (across-process) operation. As such, the API is useful in a number of applications libvorbis: libvorbis/1.3.5-GCC-6.2.0, libvorbis/1.3.5-intel-2016.u3, libvorbis/1.3.5-intel-2017.u2 libwnck: libwnck/2.26.2-intel-2016.u3, libwnck/2.30.7-intel-2016.u3 - Homepage: https://download.gnome.org/sources/libwnck/ libxc: libxc/3.0.0-intel-2016.u3, libxc/3.0.0-intel-2017.u2, libxc/3.0.0-spartan_intel-2017.u2, libxc/4.3.4-intel-2017.u2 Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals. - Homepage: http://www.tddft.org/programs/octopus/wiki/index.php/Libxc libxcb: libxcb/1.11-intel-2016.u3-Python-2.7.9, libxcb/1.11-intel-2016.u3-Python-2.7.11, libxcb/1.11.1-foss-2017b-Python-2.7.14-bare, ... The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility. - Homepage: http://xcb.freedesktop.org/ libxfce4ui: libxfce4ui/4.12.0-intel-2016.u3, libxfce4ui/4.12.1-intel-2016.u3 - Homepage: https://xfce.org/ libxfce4util: libxfce4util/4.12.1-intel-2016.u3 libxfce4util is part of xfce4 desktop - Homepage: http://xfce.org/ libxkbcommon: libxkbcommon/0.5.0-intel-2016.u3-Python-2.7.11, libxkbcommon/0.5.0-intel-2016.u3, libxkbcommon/0.5.0-intel-2017.u2, ... xkbcommon is a library to handle keyboard descriptions, including loading them from disk, parsing them and handling their state. It's mainly meant for client toolkits, window systems, and other system applications. - Homepage: http://xkbcommon.org/ libxml++: libxml++/2.40.1-intel-2017.u2, libxml++/2.40.1-spartan_gcc-6.2.0, libxml++/2.40.1-spartan_gcc-8.1.0, ... libxml++ is a C++ wrapper for the libxml XML parser library. libxml2: libxml2/2.7.8-GCC-4.9.2, libxml2/2.9.2-foss-2017b, libxml2/2.9.2-GCC-4.6.4, libxml2/2.9.2-GCC-4.9.2, libxml2/2.9.2-GCC-5.4.0, ... Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform). - Homepage: http://xmlsoft.org/ libxslt: libxslt/1.1.26-GCC-4.9.2, libxslt/1.1.28-foss-2017b, libxslt/1.1.28-GCC-4.9.2, libxslt/1.1.28-GCC-6.2.0, ... Libxslt is the XSLT C library developed for the GNOME project (but usable outside of the Gnome platform). - Homepage: http://xmlsoft.org/ libyaml: libyaml/0.1.6-intel-2016.u3, libyaml/0.1.7-intel-2017.u2-GCC-6.2.0-CUDA9, libyaml/0.1.7-intel-2017.u2-GCC-6.2.0-CUDA10, ... LibYAML is a YAML 1.1 parser and emitter written in C. - Homepage: http://pyyaml.org/wiki/LibYAML libzip: libzip/1.1.2-GCC-6.2.0, libzip/1.1.2-intel-2016.u3 libzip is a C library for reading, creating, and modifying zip archives.. - Homepage: https://nih.at/libzip/ likwid: likwid/4.2.0-foss-2017b, likwid/4.2.0-intel-2016.u3, likwid/4.2.0-intel-2017.u2, likwid/4.3.2-GCCcore-6.4.0 Likwid stands for 'Like I knew what I am doing'. Likwid is a simple to install and use toolsuite of command line applications for performance oriented programmers. It works for Intel and AMD processors on the Linux operating system. llvmlite: llvmlite/0.22.0-intel-2017.u2-Python-3.6.4 A lightweight LLVM python binding for writing JIT compilers lmoments3: lmoments3/1.0.4-intel-2017.u2-Python-3.6.4 rpy2 is Python 3.x library to estimate linear moments for statistical distribution functions. lobSTR: lobSTR/3.0.3-intel-2016.u3 lpsolve: lpsolve/5.5.2.5-intel-2016.u3, lpsolve/5.5.2.5-intel-2017.u2, lpsolve/5.5.2.5-spartan_intel-2017.u2 Mixed Integer Linear Programming (MILP) solver lsd: lsd/0.3-GCC-4.9.2 LSD: LEAST-SQUARES METHODS TO ESTIMATE RATES AND DATES FROM SERIAL PHYLOGENIES lua: lua/5.3.1-GCC-4.9.2 lxde-icon-theme: lxde-icon-theme/0.5.1-intel-2016.u3 The LXDE Icon Theme package contains nuoveXT 2.2 Icon Theme for LXDE. - Homepage: http://lxde.org/ lxml: lxml/3.6.0-intel-2016.u3-Python-2.7.9, lxml/3.6.0-intel-2016.u3-Python-2.7.10, lxml/3.6.0-intel-2016.u3-Python-3.5.2, ... The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt. lynx: lynx/2.8.7-goolf-2015a lynx is an alphanumeric display oriented World-Wide Web Client - Homepage: http://lynx.isc.org/ lz4: lz4/1.8.2-goolf-2015a, lz4/1.9.1-GCC-6.2.0, lz4/1.9.1-spartan_intel-2017.u2 LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core. It features an extremely fast decoder, with speed in multiple GB/s per core. lzma: lzma/4.32.7-foss-2017b, lzma/4.32.7-intel-2016.u3, lzma/4.32.7-intel-2017.u2 LZMA Utils are based on LZMA SDK 4.32. LZMA Utils. magma: magma/2.2.0-intel-2017.u2-GCC-5.4.0-CUDA8 The MAGMA project aims to develop a dense linear algebra library similar to LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems. make: make/4.1-GCC-4.9.2, make/4.1-GCC-6.2.0, make/4.1-gompi-2017.u1 GNU version of make utility - Homepage: http://www.gnu.org/software/make/make.html makedepend: makedepend/1.0.4-goolf-2015a, makedepend/1.0.5-GCC-4.9.2, makedepend/1.0.5-intel-2016.u3, makedepend/1.0.5-iomkl-2016.u3 The makedepend package contains a C-preprocessor like utility to determine build-time dependencies. - Homepage: http://www.linuxfromscratch.org/blfs/view/svn/x/makedepend.html mapDamage: mapDamage/2.0.9-intel-2017.u2-Python-2.7.13 mapDamage: tracking and quantifying damage patterns in ancient DNA sequences mashr: mashr/0.2-11-GCC-4.9.2 This package implements methods to estimate and test many effects in many conditions (or many effects on many outcomes). The methods use Empirical Bayes methods to estimate patterns of similarity among conditions, and then exploit those patterns of similarity among conditions to improve accuracy of effect estimates. See Urbut et al for details of the model and methods. matplotlib: matplotlib/1.5.1-intel-2016.u3-Python-2.7.9, matplotlib/1.5.1-intel-2017.u2-GCC-5.4.0-CUDA8-Python-3.5.2, ... matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits. - Homepage: http://matplotlib.org mccortex: mccortex/0.0.3 McCortex is a genome assembler and variant caller. It has a rich set of features for representing and manipulating genomes as graphs. md5deep: md5deep/4.4-intel-2016.u3 - Homepage: https://github.com/jessek/hashdeep/releases/tag/release-4.4 medaka: medaka/0.4.3-intel-2017.u2-GCC-6.2.0-CUDA9-Python-3.6.4, medaka/0.8.0-intel-2017.u2-GCC-6.2.0-CUDA9-Python-3.6.4 medaka is a tool to create a consensus sequence of nanopore sequencing data. mercury: mercury/14.01.1-GCC-4.9.2, mercury/14.01.1-intel-2016.u3 Mercury is a pure logic programming language intended for the creation of large, fast, reliable programs. - Homepage: https://www.mercurylang.org/ metaWRAP: metaWRAP/1.1-intel-2017.u2 MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation. mindboggle: mindboggle/1.2.4-intel-2017.u2-Python-3.6.1 Mindboggle’s open source brain morphometry platform takes in preprocessed T1-weighted MRI data, and outputs volume, surface, and tabular data containing label, feature, and shape information for further analysis. minia: minia/3.2.4 Minia is a short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. The output of Minia is a set of contigs. minimap2: minimap2/2.11-intel-2017.u2, minimap2/2.13-intel-2017.u2-GCC-6.2.0-CUDA9 Minimap2 is a fast sequence mapping and alignment program that can find overlaps between long noisy reads, or map long reads or their assemblies to a reference genome optionally with detailed alignment (i.e. CIGAR). At present, it works efficiently with query sequences from a few kilobases to ~100 megabases in length at an error rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limited test data sets, minimap2 is over 20 times faster than most other long-read aligners. It will replace BWA-MEM for long reads and contig alignment. mkl-dnn: mkl-dnn/0.13-intel-2018.u4 Intel(R) Math Kernel Library for Deep Neural Networks (Intel(R) MKL-DNN) mlst: mlst/2.16-spartan_intel-2017.u2 Scan contig files against traditional PubMLST typing schemes. molcas: molcas/8.2.170401-OpenMPI-2.0.2-intel-2016.u3-imkl-11.3.3.210, molcas/8.2.170401-OpenMPI-2.0.2-intel-2016.u3 Molcas is an ab initio quantum chemistry software package developed by scientists to be used by scientists. The basic philosophy is is to be able to treat general electronic structures for molecules consisting of atoms from most of the periodic table. As such, the primary focus of the package is on multiconfigurational methods with applications typically connected to the treatment of highly degenerate states. Key aspects of Molcas: SCF/DFT, CASSCF/RASSCF, CASPT2/RASPT2 Fast, accurate, and robust code Free support and updates Molcas is not a black box tool. The user should be an educated quantum chemist, with some knowledge about the different quantum chemical models in use today, their application areas and their inherent accuracy. The MOLCAS group arranges regular MOLCAS workshops, which teaches how to use the software. motif: motif/2.3.5-goolf-2015a, motif/2.3.5-intel-2016.u3 Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems. It was the standard toolkit for the Common Desktop Environment and thus for Unix. - Homepage: http://motif.ics.com/ mpj: mpj/0.44 mpmath: mpmath/0.19-intel-2016.u3-Python-2.7.11 mpmath can be used as an arbitrary-precision substitute for Python's float/complex types and math/cmath modules, but also does much more advanced mathematics. Almost any calculation can be performed just as well at 10-digit or 1000-digit precision, with either real or complex numbers, and in many cases mpmath implements efficient algorithms that scale well for extremely high precision work. - Homepage: http://mpmath.org/ mrcnn: mrcnn/2.1-intel-2017.u2-GCC-6.2.0-CUDA9-Python-3.6.4 Mask R-CNN for object detection and instance segmentation on Keras and TensorFlow ms: ms/08112017-GCC-4.9.3 The purpose of this program is to allow one to investigate the statistical properties of such samples, to evaluate estimators or statistical tests, and generally to aid in the interpretation of polymorphism data sets. mshr: mshr/2019.1.0-spartan_gcc-8.1.0 mshr is the mesh generation component of FEniCS. It generates simplicial DOLFIN meshes in 2D and 3D from geometries described by Constructive Solid Geometry (CSG) or from surface files, utilizing CGAL and Tetgen as mesh generation backends. msms: msms/3.2rc-b163-Java-1.8.0_71 MSMS is a coalescent simulator that models itself off Hudsons ms in usage and includes selection. It is fast, often faster than ms, and portable running on Mac OSX, windows and Linux. By using this tool, one can study the patterns of selection in complicated demographic scenarios. mykrobe: mykrobe/0.3.6-Python-2.7.10-bundle The Mykrobe predictor is designed for use by microbiologists and doctors, providing information needed in order to choose the best treatment. It analyses the whole genome of a bacterial sample, all within a couple of minutes, and predicts which drugs the infection is resistant to. nanopolish: nanopolish/0.9.2-intel-2017.u2 Software package for signal-level analysis of Oxford Nanopore sequencing data. ncbi-vdb: ncbi-vdb/2.9.3-spartan_intel-2017.u2 The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. ncurses: ncurses/5.9-GCC-4.6.4, ncurses/5.9-GCC-4.9.2, ncurses/5.9-GCC-4.9.3, ncurses/5.9-gompi-2015a, ncurses/5.9-goolf-2015a, ... The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses. - Homepage: http://www.gnu.org/software/ncurses/ ncview: ncview/2.1.7-intel-2016.u3 Ncview is a visual browser for netCDF format files. Typically you would use ncview to get a quick and easy, push-button look at your netCDF files. You can view simple movies of the data, view along various dimensions, take a look at the actual data values, change color maps, invert the data, etc. - Homepage: http://meteora.ucsd.edu/~pierce/ncview_home_page.html netCDF: netCDF/4.3.2-GCC-4.9.2, netCDF/4.3.2-intel-2016.u3, netCDF/4.4.0-foss-2017b, netCDF/4.4.0-intel-2016.u3, ... NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. - Homepage: http://www.unidata.ucar.edu/software/netcdf/ netCDF-C++: netCDF-C++/4.2-foss-2017b, netCDF-C++/4.2-intel-2017.u2-GCC-6.2.0-CUDA9.1 NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. netCDF-Fortran: netCDF-Fortran/4.4.0-GCC-4.9.2, netCDF-Fortran/4.4.0-intel-2016.u3, netCDF-Fortran/4.4.3-foss-2017b, ... NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. netcdf4-python: netcdf4-python/1.3.1-intel-2017.u2-Python-3.6.4-HDF5-1.8.19 Python/numpy interface to netCDF. nettle: nettle/3.2-foss-2017b, nettle/3.2-GCC-4.9.2, nettle/3.2-GCC-6.2.0, nettle/3.2-intel-2016.u3, ... Nettle is a cryptographic library that is designed to fit easily in more or less any context: In crypto toolkits for object-oriented languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, or even in kernel space. - Homepage: http://www.lysator.liu.se/~nisse/nettle/ networkx: networkx/2.2-intel-2017.u2-Python-3.6.4 NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks. newick-utils: newick-utils/1.6-spartan_intel-2017.u2 The Newick Utilities are a suite of Unix shell tools for processing phylogenetic trees. We distribute the package under the BSD License. Functions include re-rooting, extracting subtrees, trimming, pruning, condensing, drawing (ASCII graphics or SVG). newmat: newmat/11-spartan_gcc-6.2.0, newmat/11-spartan_intel-2017.u2 This C++ library is intended for scientists and engineers who need to manipulate a variety of types of matrices using standard matrix operations. Emphasis is on the kind of operations needed in statistical calculations such as least squares, linear equation solve and eigenvalues. ngs-bits: ngs-bits/2019_04-spartan_gcc-6.2.0 ngs-bits - Short-read sequencing tools nomacs: nomacs/3.12-intel-2017.u2 nomacs is a free, open source image viewer, which supports multiple platforms. You can use it for viewing all common image formats including RAW and psd images. norgal: norgal/1.0-GCC-6.2.0-Python-3.7.1 Norgal takes NGS sequencing reads as input and tries to assemble the mitochondrial genome using kmer frequencies. ns: ns/3.27-GCC-4.9.2 Ns-3 is a discrete event simulator targeted at networking research. nullarbor: nullarbor/2.0.20181010-spartan_intel-2017.u2 Pipeline to generate complete public health microbiology reports from sequenced isolates. numactl: numactl/2.0.10-GCC-4.6.4, numactl/2.0.10-GCC-4.9.2, numactl/2.0.10-GNU-4.9.2-2.25, numactl/2.0.10, numactl/2.0.11-GCC-4.9.2, ... numba: numba/0.36.2-intel-2017.u2-Python-3.6.4 numexpr: numexpr/2.6.4-intel-2017.u2-Python-3.6.4 The numexpr package evaluates multiple-operator array expressions many times faster than NumPy can. It accepts the expression as a string, analyzes it, rewrites it more efficiently, and compiles it on the fly into code for its internal virtual machine (VM). Due to its integrated just-in-time (JIT) compiler, it does not require a compiler at runtime. numpy: numpy/1.8.2-intel-2016.u3-Python-2.7.9, numpy/1.8.2-intel-2016.u3-Python-2.7.10, numpy/1.8.2-intel-2016.u3-Python-2.7.11, ... NumPy is the fundamental package for scientific computing with Python. It contains among other things: a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases. nvptx-tools: nvptx-tools/1.0-GCCcore-8.2.0 nvptx-tools: a collection of tools for use with nvptx-none GCC toolchains. ont-guppy: ont-guppy/3.1.5 Guppy software supports MinIT and MinION instruments from Nanopore Technologies openslide: openslide/3.4.1-intel-2017.u2 This library reads whole slide image files (also known as virtual slides). It provides a consistent and simple API for reading files from multiple vendors. orfm: orfm/0.7.1 A simple and not slow open reading frame (ORF) caller. No bells or whistles like frameshift detection, just a straightforward goal of returning a FASTA file of open reading frames over a certain length from a FASTA/Q file of nucleotide sequences. p7zip: p7zip/16.02-intel-2017.u2 p7zip is a quick port of 7z.exe and 7za.exe (command line version of 7zip) for Unix. 7-Zip is a file archiver with highest compression ratio. pandas: pandas/0.18.1-intel-2016.u3-Python-3.5.2, pandas/0.23.4-goolf-2015a-Python-2.7.12, pandas/0.23.4-intel-2016.u3-Python-3.5.2 Powerful data structures for data analysis, time series,and statistics pandoc: pandoc/2.0.3, pandoc/2.5 Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. parallel: parallel/20141122-GCC-4.9.2, parallel/20141122-intel-2016.u3, parallel/20150322-GCC-4.9.2, parallel/20170206-foss-2017b, ... parsnp: parsnp/1.2 Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. patchelf: patchelf/0.8-GNU-4.9.2-2.25, patchelf/0.10-spartan_gcc-8.1.0 PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables. petsc4py: petsc4py/3.6.0-intel-2016.u3-Python-2.7.9, petsc4py/3.6.0-intel-2016.u3-Python-2.7.11, ... petsc4py are Python bindings for PETSc, the Portable, Extensible Toolchain for Scientific Computation. picard: picard/1.127, picard/2.3.0, picard/2.6.0, picard/2.18.27 A set of tools (in Java) for working with next generation sequencing data in the BAM format. pigz: pigz/2.4-spartan_intel-2017.u2 pigz, which stands for Parallel Implementation of GZip, is a fully functional replacement for gzip that exploits multiple processors and multiple cores to the hilt when compressing data. pilon: pilon/1.21-Java-1.8.0_71, pilon/1.21-Java-1.8.0_152 Pilon is a software tool which can be used to: Automatically improve draft assemblies Find variation among strains, including large event detection pinfish: pinfish/20181106 Pinfish is a collection of tools helping to make sense of long transcriptomics data (long cDNA reads, direct RNA reads). pixman: pixman/0.32.6-foss-2017b, pixman/0.32.6-GCC-4.9.2, pixman/0.32.6-GCC-6.2.0, pixman/0.32.6-GCCcore-6.4.0, ... pkg-config: pkg-config/0.29-GCC-4.9.2, pkg-config/0.29-goolf-2015a, pkg-config/0.29-intel-2016.u3, ... pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the correct compiler options on the command line so an application can use gcc -o test test.c `pkg-config --libs --cflags glib-2.0` for instance, rather than hard-coding values on where to find glib (or other libraries). - Homepage: http://www.freedesktop.org/wiki/Software/pkg-config/ pkgconfig: pkgconfig/1.2.2-intel-2017.u2-Python-2.7.13 pkgconfig is a Python module to interface with the pkg-config command line tool plastimatch: plastimatch/1.80-spartan_gcc-6.2.0 Plastimatch is an open source software for image computation. Our main focus is high-performance volumetric registration, segmentation, and image processing of volumetric medical images. plotly: plotly/1.12.2-intel-2016.u3-Python-3.5.2, plotly/3.2.1-intel-2017.u2-Python-3.6.4 Python plotting library for collaborative, interactive, publication-quality graphs. plotly.py: plotly.py/4.7.1-intel-2017.u2-Python-3.6.4 An open-source, interactive graphing library for Python plumed: plumed/2.2.3-intel-2016.u3, plumed/2.6.0-intel-2017.u2 PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. poretools: poretools/0.6.0-intel-2017.u2-Python-2.7.13 A toolkit for working with nanopore sequencing data from Oxford Nanopore. pplacer: pplacer/1.1 Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment. printproto: printproto/1.0.5-intel-2016.u3, printproto/1.0.5-spartan_intel-2017.u2 X.org PrintProto protocol headers. - Homepage: http://xorg.freedesktop.org/ prodigal: prodigal/2.6.2-spartan_intel-2017.u2 Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee. prokka: prokka/1.13-spartan_gcc-6.2.0, prokka/1.13-spartan_intel-2017.u2, prokka/1.14.0-spartan_intel-2017.u2 Prokka is a software tool for the rapid annotation of prokaryotic genomes. protobuf: protobuf/2.6.1-GCC-4.9.2, protobuf/2.6.1-GCC-6.2.0, protobuf/2.6.1-intel-2016.u3, protobuf/2.6.1, protobuf/3.3.0-GCC-4.9.2, ... protobuf-python: protobuf-python/3.3.0-intel-2016.u3-Python-3.5.2, protobuf-python/3.3.0-intel-2017.u2-GCC-5.4.0-CUDA8-Python-3.5.2, ... Python Protocol Buffers runtime library. - Homepage: https://github.com/google/protobuf/ psycopg2: psycopg2/2.7.5-goolf-2015a-Python-2.7.12 Psycopg is the most popular PostgreSQL adapter for the Python programming language. At its core it fully implements the Python DB API 2.0 specifications. pullseq: pullseq/1.0.2-spartan_intel-2017.u2 Software to extract sequence from a fasta or fastq. Also filter sequences by a minimum length or maximum length. Fast, written in C, using kseq.h library. pyMESS: pyMESS/0.32.1-spartan_intel-2017.u2-Python-2.7.13 pyMESS is python package for MESS pybedtools: pybedtools/0.7.10-intel-2017.u2-Python-3.6.4 Wrapper around BEDTools for bioinformatics work pybind11: pybind11/2.2.4-spartan_gcc-6.2.0, pybind11/2.2.4-spartan_gcc-8.1.0-Python-3.7.3, pybind11/2.3.0-spartan_gcc-6.2.0 DOLFIN is the computational backend of FEniCS and implements the FEniCS Problem Solving Environment in Python and C++. pychopper: pychopper/0.2.0-intel-2017.u2-Python-3.5.2 A tool to identify full length cDNA reads. pydicom: pydicom/0.9.9-intel-2016.u3-Python-2.7.9 Read, modify and write DICOM files with python code - Homepage: https://github.com/darcymason/pydicom pyngl: pyngl/1.6.1-spartan_intel-2017.u2-Python-3.6.4 PyNGL ("pingle") is a Python module built on top of NCL's graphics library, which produces publication-quality, two-dimensional visualizations tailored for climate and weather data. pysc2: pysc2/2.0.1-intel-2017.u2-GCC-6.2.0-CUDA9-Python-3.6.4 StarCraft II Learning Environment pyseer: pyseer/1.1.2-intel-2017.u2-Python-3.6.4 SEER, reimplemented in python pyshp: pyshp/1.2.12-goolf-2015a-Python-2.7.12 The dateutil module provides powerful extensions to the datetime module available in the Python standard library. - Homepage: https://pypi.python.org/pypi/python-dateutil pysqlite: pysqlite/2.6.3-intel-2016.u3-Python-2.7.9, pysqlite/2.6.3-spartan_intel-2017.u2-Python-2.7.13 pysqlite is an interface to the SQLite 3.x embedded relational database engine. It is almost fully compliant with the Python database API version 2.0 also exposes the unique features of SQLite. - Homepage: https://pypi.python.org/pypi/pysqlite pytest: pytest/4.4.0-spartan_gcc-8.1.0-Python-3.7.3 pytest: simple powerful testing with Python python-dateutil: python-dateutil/2.6.1-goolf-2015a-Python-2.7.12 The dateutil module provides powerful extensions to the datetime module available in the Python standard library. - Homepage: https://pypi.python.org/pypi/python-dateutil quicktree: quicktree/2.0-spartan_intel-2017.u2, quicktree/2.4-spartan_intel-2017.u2 QuickTree is an efficient implementation of the Neighbor-Joining algorithm (PMID: 3447015), capable of reconstructing phylogenies from huge alignments in time less than the age of the universe. rainbow: rainbow/2.0.4-foss-2017b, rainbow/2.0.4-intel-2017.u2 Efficient tool for clustering and assembling short reads, especially for RAD. randrproto: randrproto/1.5.0-intel-2016.u3, randrproto/1.5.0-intel-2017.u2 Xrandr protocol and ancillary headers - Homepage: http://www.freedesktop.org/wiki/Software/xlibs rconnector: rconnector/1.2.0 Short read connector enables the comparisons of two read sets B and Q. recentrifuge: recentrifuge/20181019-intel-2017.u2 Robust comparative analysis and contamination removal for metagenomics redis: redis/5.0.3-GCC-6.2.0 Redis is an open source (BSD licensed), in-memory data structure store, used as a database, cache and message broker. renderproto: renderproto/0.11-intel-2016.u3, renderproto/0.11-intel-2017.u2, renderproto/0.11-iomkl-2016.u3 Xrender protocol and ancillary headers - Homepage: http://www.freedesktop.org/wiki/Software/xlibs requests: requests/2.7.0-intel-2016.u3-Python-2.7.9, requests/2.11.1-intel-2016.u3-Python-2.7.10, ... Python http for humans rpy2: rpy2/2.9.4-intel-2017.u2-Python-3.6.4, rpy2/2.9.4-spartan_gcc-6.2.0-Python-3.6.4 rpy2 is a redesign and rewrite of rpy. It is providing a low-level interface to R from Python, a proposed high-level interface, including wrappers to graphical libraries, as well as R-like structures and functions. ruffus: ruffus/2.6.3-intel-2016.u3-Python-2.7.10 The Ruffus module is a lightweight way to add support for running computational pipelines. samclip: samclip/0.2 Filter SAM file for soft and hard clipped alignments scikit-image: scikit-image/0.13.1-intel-2017.u2-Python-2.7.13, scikit-image/0.14.0-intel-2017.u2-Python-3.6.4 scikit-image is a collection of algorithms for image processing. It is available free of charge and free of restriction. We pride ourselves on high-quality, peer-reviewed code, written by an active community of volunteers. scikit-learn: scikit-learn/0.18-intel-2016.u3-Python-2.7.9, scikit-learn/0.18-intel-2017.u2-GCC-5.4.0-CUDA8-Python-3.5.2, ... Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. It strives to be simple and efficient, accessible to everybody, and reusable in various contexts. - Homepage: http://scikit-learn.org/stable/index.html scrm: scrm/1.7.2-GCC-4.9.2 scrm simulates the evolution of genetic sequences. It takes a neutral evolutionary model as input, and generates random sequences that evolved under the model. As coalescent simulator, it traces the ancestry of the sampled sequences backwards in time and is therefore extremely efficient. Compared to other coalescent simulators, it can simulate chromosome-scale sequences without a measureable reduction of genetic linkage between different sites. sdsl-lite: sdsl-lite/2.0.3-spartan_intel-2017.u2 The Succinct Data Structure Library (SDSL) is a powerful and flexible C++11 library implementing succinct data structures. In total, the library contains the highlights of 40 research publications. semtex: semtex/9.1-intel-2017.u2 Semtex is a 'classical' quadrilateral spectral element DNS code that uses the standard nodal GLL basis functions and (optionally) Fourier expansions in a homogeneous direction to provide three-dimensional solutions. If your problem has a natural periodic coordinate direction in 3D (a cylindrical coordinate system is perhaps the most obvious example), semtex could be a good choice. For 3D problems of this kind, the code can run in parallel using MPI to distribute jobs over a number of processes; semtex is equally at home on Unix machines from laptop to supercomputer. seqtk: seqtk/1.2-r94-intel-2016.u3 Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. sharedmem: sharedmem/0.3.5-intel-2017.u2-Python-3.6.4 A different flavor of multiprocessing in Python shovill: shovill/1.0.0-spartan_intel-2017.u2, shovill/1.0.4-spartan_intel-2017.u2, shovill/1.0.9-spartan_intel-2017.u2 Assemble bacterial isolate genomes from Illumina paired-end reads. showq: showq/0.12, showq/0.15 simka: simka/1.5.2 Simka is a de novo comparative metagenomics tool. Simka represents each dataset as a k-mer spectrum and compute several classical ecological distances between them. slepc4py: slepc4py/3.6.0-intel-2016.u3-Python-2.7.9, slepc4py/3.6.0-intel-2016.u3-Python-2.7.11, ... Python bindings for SLEPc, the Scalable Library for Eigenvalue Problem Computations. slurm: slurm/latest slurm_drmaa: slurm_drmaa/1.0.7-GCC-4.9.2, slurm_drmaa/1.10.0-GCC-4.9.2 smafa: smafa/0.1.2 Smafa attempts to align or cluster pre-aligned biological sequences, handling sequences which are all the same length. smart-open: smart-open/1.8.0-intel-2016.u3-Python-2.7.12, smart-open/1.8.0-intel-2017.u2-Python-2.7.13 Scalable statistical semantics, Analyze plain-text documents for semantic structure, Retrieve semantically similar documents snakemake: snakemake/5.3.0-intel-2017.u2-Python-3.6.4 The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. snappy: snappy/1.1.6-intel-2017.u2-GCC-5.4.0-CUDA8, snappy/1.1.6, snappy/1.1.7-intel-2017.u2 Snappy is a compression/decompression library. It does not aim for maximum compression, or compatibility with any other compression library; instead, it aims for very high speeds and reasonable compression. snippy: snippy/4.4.1-spartan_intel-2017.u2 Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. snp-dists: snp-dists/0.6.3-spartan_intel-2017.u2 Convert a FASTA alignment to SNP distance matrix. snp-sites: snp-sites/2.4.1-spartan_intel-2017.u2 Rapidly decreasing genome sequencing costs have led to a proportionate increase in the number of samples used in prokaryotic population studies. snpEff: snpEff/4.1d-Java-1.7.0_80, snpEff/4.2-Java-1.8.0_71, snpEff/4.3-Java-1.8.0_71 SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes). sparsehash: sparsehash/2.0.2-goolf-2015a, sparsehash/2.0.3-intel-2016.u3 An extremely memory-efficient hash_map implementation. 2 bits/entry overhead! The SparseHash library contains several hash-map implementations, including implementations that optimize for space or speed. spartan: spartan/2016-03-parallel, spartan/2016-03 spartan-gpgpu: spartan-gpgpu/2018.u4 Intel Cluster Toolchain Compiler Edition Intel C/C++ and Fortran compilers, Intel MKL, plus nVidia CUDA. With added OpenMPI using ucx, tuned for Spartan's gpgpu cluster. spartan_gcc: spartan_gcc/6.2.0-cuda9.2, spartan_gcc/6.2.0, spartan_gcc/8.1.0 Spartan GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK. spartan_gompi: spartan_gompi/GCC-6.2.0-OpenMPI-3.0.0, spartan_gompi/GCC-6.2.0-OpenMPI-3.1.0-cuda9.2, ... GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support. spartan_intel: spartan_intel/2017.u2-cuda9.1, spartan_intel/2017.u2 Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI. speedseq: speedseq/0.1.2-GCC-6.2.0 A flexible framework for rapid genome analysis and interpretation startup-notification: startup-notification/0.12-intel-2016.u3 startup-notification contains a reference implementation of the startup notification protocol. The reference implementation is mostly under an X Window System style license, and has no special dependencies. - Homepage: http://www.freedesktop.org/wiki/Software/startup-notification statsmodels: statsmodels/0.9.0-intel-2017.u2-Python-3.6.4 statsmodels is a Python module that provides classes and functions for the estimation of many different statistical models, as well as for conducting statistical tests, and statistical data exploration. stubb: stubb/2.1-spartan_gcc-6.2.0-REforge For finding cis-regulatory modules - NB: this version patched for use with REforge. supernova: supernova/2.1.1 Supernova is a software package for de novo assembly from Chromium Linked-Reads that are made from a single whole-genome library from an individual DNA source sympy: sympy/0.7.6-goolf-2015a-Python-2.7.10, sympy/0.7.6-intel-2016.u3-Python-2.7.9, sympy/0.7.6-intel-2016.u3-Python-2.7.10, ... SymPy is a Python library for symbolic mathematics. It aims to become a full-featured computer algebra system (CAS) while keeping the code as simple as possible in order to be comprehensible and easily extensible. SymPy is written entirely in Python and does not require any external libraries. tabix: tabix/0.2.6-foss-2017b, tabix/0.2.6-GCCcore-6.4.0, tabix/0.2.6-intel-2016.u3, tabix/0.2.6-intel-2017.u2, ... Generic indexer for TAB-delimited genome position files tagcleaner: tagcleaner/0.16-spartan_gcc-6.2.0 The TagCleaner tool can be used to automatically detect and efficiently remove tag sequences (e.g. WTA tags) from genomic and metagenomic datasets. Go to http://tagcleaner.sourceforge.net/ for access to a user-friendly web-interface, the documentation and the latest updates.TagCleaner will help you to preprocess your genomic or metagenomic sequence data in FASTA or FASTQ format. taxator-tk: taxator-tk/1.3.3-intel-2016.u3-Python-2.7.11, taxator-tk/1.3.3-intel-2017.u2-Python-2.7.11 A set of programs for the taxonomic analysis of nucleotide sequence data . tbb: tbb/2017_U5-intel-2017.u2, tbb/2019_U9-spartan_gcc-6.2.0 Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that take full advantage of multicore performance, that are portable, composable and have future-proof scalability. tbl2asn: tbl2asn/24.3, tbl2asn/24.9, tbl2asn/25.0, tbl2asn/25.8 tcsh: tcsh/6.18.01-intel-2016.u3, tcsh/6.20.00-intel-2017.u2, tcsh/6.20.00-spartan_intel-2017.u2 Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). It is a command language interpreter usable both as an interactive login shell and a shell script command processor. It includes a command-line editor, programmable word completion, spelling correction, a history mechanism, job control and a C-like syntax. - Homepage: http://www.tcsh.org texinfo: texinfo/6.5-GCC-6.2.0 Texinfo is the official documentation format of the GNU project. texlive: texlive/2017-GCC-4.9.2, texlive/2017-GCC-6.2.0 TeX Live is an easy way to get up and running with the TeX document production system. It provides a comprehensive TeX system with binaries for most flavors of Unix, including GNU/Linux, and also Windows. It includes all the major TeX-related programs, macro packages, and fonts that are free software, including support for many languages around the world. tmux: tmux/2.9a-GCC-6.2.0 tmux is a terminal multiplexer. It lets you switch easily between several programs in one terminal, detach them (they keep running in the background) and reattach them to a different terminal. And do a lot more. torchvision: torchvision/0.4.0-intel-2017.u2-GCC-6.2.0-CUDA10-Python-3.6.4 Datasets, Transforms and Models specific to Computer Vision trimAI: trimAI/1.4.1-spartan_gcc-6.2.0 Multiple sequence alignments (MSA) are central to many areas of bioinformatics and evolutionary biology. tumbler: tumbler/0.1.31-intel-2016.u3 - Homepage: http:/xfce.org/ unicycler: unicycler/0.4.7-GCC-6.2.0-Python-3.5.2 Unicycler is a hybrid assembly pipeline for bacterial genomes. It uses both Illumina reads and long reads (PacBio or Nanopore) to produce complete and accurate assemblies unimelb-mf-clients: unimelb-mf-clients/current unimelb-mf-clients is a collection of command-line tools to transfer data to/from Mediaflux, the data management platform operated by Research Computing Services unixODBC: unixODBC/2.3.4-GCC-4.9.2 unrar: unrar/5.7.3-GCC-6.2.0 RAR is a powerful archive manager. urllib3: urllib3/1.24.1-GCC-6.2.0 HTTP library with thread-safe connection pooling, file post, and more utf8proc: utf8proc/2.4.0-GCC-6.2.0, utf8proc/2.4.0-spartan_intel-2017.u2 utf8proc is a small, clean C library that provides Unicode normalization, case-folding, and other operations for data in the UTF-8 encoding. util-linux: util-linux/2.26.1-intel-2016.u3, util-linux/2.28-goolf-2015a, util-linux/2.28-intel-2016.u3, ... Set of Linux utilities - Homepage: http://www.kernel.org/pub/linux/utils/util-linux vcfanno: vcfanno/0.3.1 vcfanno allows you to quickly annotate your VCF with any number of INFO fields from any number of VCFs or BED files. vcflib: vcflib/1.0.0-rc2-intel-2017.u2 A C++ library for parsing and manipulating VCF files. vsearch: vsearch/2.0.3-goolf-2015a, vsearch/2.0.3-intel-2016.u3, vsearch/2.4.3-goolf-2015a, vsearch/2.4.3-intel-2016.u3 The aim of this project is to create an alternative to the USEARCH tool developed by Robert C. Edgar (2010). vt: vt/0.577-intel-2017.u2 A tool set for short variant discovery in genetic sequence data. vtk_cpp_tools: vtk_cpp_tools/7.1.1-intel-2017.u2 web_proxy: web_proxy/latest wget: wget/1.19.4-GCC-8.2.0, wget/1.19.4-intel-2016.u3, wget/1.19.4-spartan_gcc-6.2.0, wget/1.19.4-spartan_intel-2017.u2 GNU Wget is a free software package for retrieving files using HTTP, HTTPS and FTP, the most widely-used Internet protocols. It is a non-interactive commandline tool, so it may easily be called from scripts, cron jobs, terminals without X-Windows support, etc. wheel: wheel/0.32.1-spartan_intel-2017.u2-Python-2.7.13, wheel/0.33.1-intel-2017.u2-GCC-6.2.0-CUDA9-Python-3.6.4, ... This library is the reference implementation of the Python wheel packaging standard, as defined in PEP 427. wxPython: wxPython/3.0.2.0-intel-2017.u2-Python-2.7.13 wxPython is a GUI toolkit for the Python programming language. It allows Python programmers to create programs with a robust, highly functional graphical user interface, simply and easily. It is implemented as a Python extension module (native code) that wraps the popular wxWidgets cross platform GUI library, which is written in C++. wxWidgets: wxWidgets/3.0.2-intel-2017.u2, wxWidgets/3.1.0-GCC-4.9.2, wxWidgets/3.1.0-intel-2017.u2 wxWidgets is a C++ library that lets developers create GUI applications. x264: x264/20160614-GCC-4.9.2, x264/20160614-intel-2016.u3, x264/20160614-intel-2017.u2-GCC-5.4.0-CUDA8, ... x264 is a free software library and application for encoding video streams into the H.264/MPEG-4 AVC compression format, and is released under the terms of the GNU GPL. x265: x265/2.9-GCC-6.2.0, x265/2.9-intel-2017.u2, x265/2.9-spartan_gcc-6.2.0-cuda9.2, x265/2.9-spartan_gcc-6.2.0, ... x265 is a free software library and application for encoding video streams into the H.265 AVC compression format, and is released under the terms of the GNU GPL. xapian: xapian/1.4.11-GCC-6.2.0 xapian-bindings: xapian-bindings/1.4.11-GCC-6.2.0 Xapian is an Open Source Search Engine Library, released under the GPL v2+. It's written in C++, with bindings to allow use from Perl, Python 2, Python 3, PHP 5, PHP 7, Java, Tcl, C#, Ruby, Lua, Erlang, Node.js and R (so far!) xapian-core: xapian-core/1.4.11-GCC-6.2.0 Xapian is an Open Source Search Engine Library, released under the GPL v2+. It's written in C++, with bindings to allow use from Perl, Python 2, Python 3, PHP 5, PHP 7, Java, Tcl, C#, Ruby, Lua, Erlang, Node.js and R (so far!) xapian-omega: xapian-omega/1.4.11-GCC-6.2.0 Xapian is an Open Source Search Engine Library, released under the GPL v2+. It's written in C++, with bindings to allow use from Perl, Python 2, Python 3, PHP 5, PHP 7, Java, Tcl, C#, Ruby, Lua, Erlang, Node.js and R (so far!) xbitmaps: xbitmaps/1.1.1-goolf-2015a, xbitmaps/1.1.1-intel-2016.u3 provides bitmaps for x - Homepage: http://www.freedesktop.org/wiki/Software/xlibs xcb-proto: xcb-proto/1.11-foss-2017b-Python-2.7.14-bare, xcb-proto/1.11-foss-2017b-Python-2.7.14, ... The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility. xcb-util: xcb-util/0.4.0-intel-2016.u3-Python-2.7.11, xcb-util/0.4.0-intel-2016.u3, xcb-util/0.4.0-intel-2017.u2, ... The xcb-util package provides additional extensions to the XCB library, many that were previously found in Xlib, but are not part of core X protocol - Homepage: http://xcb.freedesktop.org/ xcb-util-image: xcb-util-image/0.4.0-intel-2016.u3-Python-2.7.11, xcb-util-image/0.4.0-intel-2016.u3, ... The xcb-util-image package provides additional extensions to the XCB library. - Homepage: http://xcb.freedesktop.org/ xcb-util-keysyms: xcb-util-keysyms/0.4.0-intel-2016.u3, xcb-util-keysyms/0.4.0-intel-2017.u2, xcb-util-keysyms/0.4.0-iomkl-2016.u3 The xcb-util-keysyms package contains a library for handling standard X key constants and conversion to/from keycodes. - Homepage: http://xcb.freedesktop.org/ xcb-util-renderutil: xcb-util-renderutil/0.3.9-intel-2016.u3-Python-2.7.11, xcb-util-renderutil/0.3.9-intel-2016.u3, ... The xcb-util-renderutil package provides additional extensions to the XCB library. - Homepage: http://xcb.freedesktop.org/ xcb-util-wm: xcb-util-wm/0.4.1-intel-2016.u3-Python-2.7.11, xcb-util-wm/0.4.1-intel-2016.u3, xcb-util-wm/0.4.1-intel-2017.u2, ... The xcb-util-wm package contains libraries which provide client and window-manager helpers for EWMH and ICCCM. - Homepage: http://xcb.freedesktop.org/ xdrfile: xdrfile/1.1.4-intel-2017.u2-GCC-6.2.0-CUDA9.1 The plan is here to make a separate library for reading and writing xtc, edr and trr files, which will be distributed under the lesser GNU public license. xextproto: xextproto/7.3.0-foss-2017b, xextproto/7.3.0-GCC-4.9.2, xextproto/7.3.0-GCC-6.2.0, xextproto/7.3.0-goolf-2015a, ... XExtProto protocol headers. - Homepage: http://www.freedesktop.org/wiki/Software/xlibs xf86vidmodeproto: xf86vidmodeproto/2.3.1-GCC-6.2.0 X11 XFree86 video mode extension protocol headers. xfce4: xfce4/4.12-intel-2016.u3 xfce4-appfinder: xfce4-appfinder/4.12.0-intel-2016.u3 - Homepage: http:/xfce.org/ xfce4-panel: xfce4-panel/4.12.0-intel-2016.u3 - Homepage: http:/xfce.org/ xfce4-session: xfce4-session/4.12.1-intel-2016.u3 - Homepage: http://xfce.org xfce4-settings: xfce4-settings/4.12.1-intel-2016.u3 - Homepage: http://xfce.com xfconf: xfconf/4.12.0-intel-2016.u3 - Homepage: https://xfce.org/ xfdesktop: xfdesktop/4.12.0-intel-2016.u3 xfce4 Desktop - Homepage: http://xfce.org xfwm4: xfwm4/4.12.0-intel-2016.u3 xfce4 Window Manager - Homepage: http://xfce.org xineramaproto: xineramaproto/1.2.1-intel-2016.u3, xineramaproto/1.2.1-intel-2017.u2 X protocol and ancillary headers for xinerama - Homepage: http://www.freedesktop.org/wiki/Software/xlibs xorg-macros: xorg-macros/1.17-foss-2017b, xorg-macros/1.17-GCC-4.9.2, xorg-macros/1.17-GCC-6.2.0, xorg-macros/1.17-goolf-2015a, ... xplor-nih: xplor-nih/2.47 XPLOR-NIH is a structure determination program which builds on the X-PLOR program, including additional tools developed at the NIH. xprop: xprop/1.2.2-intel-2016.u3, xprop/1.2.2-intel-2017.u2-GCC-6.2.0-CUDA9, xprop/1.2.2-intel-2017.u2, ... The xprop utility is for displaying window and font properties in an X server. One window or font is selected using the command line arguments or possibly in the case of a window, by clicking on the desired window. A list of properties is then given, possibly with formatting information. - Homepage: http://www.x.org/wiki/ xproto: xproto/7.0.27-GCC-4.9.2, xproto/7.0.27-intel-2016.u3, xproto/7.0.27-intel-2017.u2, xproto/7.0.28-foss-2017b, ... X protocol and ancillary headers - Homepage: http://www.freedesktop.org/wiki/Software/xlibs xtrans: xtrans/1.3.5-foss-2017b, xtrans/1.3.5-GCC-4.9.2, xtrans/1.3.5-GCC-6.2.0, xtrans/1.3.5-goolf-2015a, xtrans/1.3.5-intel-2016.u3, ... xtrans includes a number of routines to make X implementations transport-independent; at time of writing, it includes support for UNIX sockets, IPv4, IPv6, and DECnet. - Homepage: http://www.freedesktop.org/wiki/Software/xlibs yajl: yajl/2.1.0-GCC-4.9.2 Yet Another JSON Library (YAJL) is a C library for parsing JSON yaml-cpp: yaml-cpp/0.6.3-spartan_intel-2017.u2 yaml-cpp is a YAML parser and emitter in C++ matching the YAML 1.2 spec. zlib: zlib/1.2.7-intel-2016.u3, zlib/1.2.8-foss-2017b, zlib/1.2.8-GCC-4.6.4, zlib/1.2.8-GCC-4.9.2-binutils-2.25, zlib/1.2.8-GCC-4.9.2, ... zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system. zsh: zsh/5.2 Zsh is a shell designed for interactive use, although it is also a powerful scripting language. zstd: zstd/1.3.4-goolf-2015a Zstandard is a real-time compression algorithm, providing high compression ratios. It offers a very wide range of compression/speed trade-off, while being backed by a very fast decoder. It also offers a special mode for small data, called dictionary compression, and can create dictionaries from any sample set. zsync: zsync/0.6.2-goolf-2015a zsync-0.6.2: Optimising file distribution program, a 1-to-many rsync ---------------------------------------------------------------------------------------------------------------------------------------- To learn more about a package execute: $ module spider Foo where "Foo" is the name of a module. To find detailed information about a particular package you must specify the version if there is more than one version: $ module spider Foo/11.1 ---------------------------------------------------------------------------------------------------------------------------------------- ************************************************************** Software list using 2019+ build system ************************************************************** ---------------------------------------------------------------------------------------------------------------------------------------- The following is a list of the modules and extensions currently available: ---------------------------------------------------------------------------------------------------------------------------------------- EasyBuild: EasyBuild/latest, EasyBuild/3.9.3, EasyBuild/4.0.1, EasyBuild/4.1.1, EasyBuild/4.2.0, EasyBuild/4.3.0, EasyBuild/4.3.1, ... EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way. abaqus: abaqus/2017-hotfix-1721 Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA. abricate: abricate/0.9.9-perl-5.30.0 Mass screening of contigs for antimicrobial and virulence genes abyss: abyss/2.1.5 Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler act: act/18.0.2-java-11.0.2 ACT is a Java application for displaying pairwise comparisons between two or more DNA sequences. It can be used to identify and analyse regions of similarity and difference between genomes and to explore conservation of synteny, in the context of the entire sequences and their annotation. It can read complete EMBL, GENBANK and GFF entries or sequences in FASTA or raw format. actc: actc/1.1 ACTC converts independent triangles into triangle strips or fans. admixture: admixture/1.3.0 ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm. afni: afni/18.3.00-python-3.7.4 AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity. ale: ale/20180904 You can convert the .ale file to a set of .wig files with ale2wiggle.py and IGV can read those directly. alf: alf/2.1 Absorption Line Fitter, alf, is a program for fitting the absorption line optical—NIR spectrum of an old (& 1 Gyr) stellar system. allelecount: allelecount/3.3.1 almosthere: almosthere/1.0.10 Progress indicator C library. ATHR is a simple yet powerful progress indicator library that works on Windows, Linux, and macOS. It is non-blocking as the progress update is done via a dedicated, lightweight thread, as to not impair the performance of the calling program. anaconda2: anaconda2/2019.10 Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture. anaconda3: anaconda3/5.3.0, anaconda3/2020.02, anaconda3/2020.07, anaconda3/2020.11 Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture. ansys_cfd: ansys_cfd/20.1 ANSYS computational fluid dynamics (CFD) simulation software allows you to predict, with confidence, the impact of fluid flows on your product throughout design and manufacturing as well as during end use. ANSYS renowned CFD analysis tools include the widely used and well-validated ANSYS Fluent and ANSYS CFX. ant: ant/1.10.0-java-1.8.0_241, ant/1.10.5-java-1.8.0_241, ant/1.10.7-java-11.0.2 Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications. antlr: antlr/2.7.7 ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) is a language tool that provides a framework for constructing recognizers, compilers, and translators from grammatical descriptions containing Java, C#, C++, or Python actions. ants: ants/2.3.2-python-3.7.4 ANTs extracts information from complex datasets that include imaging. ANTs is useful for managing, interpreting and visualizing multidimensional data. any2fasta: any2fasta/0.4.2 Convert various sequence formats to FASTA apex: apex/20200325-python-3.7.4 A PyTorch Extension: Tools for easy mixed precision and distributed training in Pytorch apr: apr/1.7.0 Apache Portable Runtime (APR) libraries. apr-util: apr-util/1.6.1 Apache Portable Runtime (APR) util libraries. archspec: archspec/0.1.0-python-3.7.4 A library for detecting, labeling, and reasoning about microarchitectures argtable: argtable/2.13 Argtable is an ANSI C library for parsing GNU style command line options with a minimum of fuss. armadillo: armadillo/9.700.2, armadillo/10.3.0 Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. armatus: armatus/2.3 Multiresolution domain calling software for chromosome conformation capture interaction matrices. arpack-ng: arpack-ng/3.7.0 ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. asap: asap/1.9-python-3.7.4 Program for the analysis and visualization of whole-slide images in digital pathology. at-spi2-atk: at-spi2-atk/2.34.1 AT-SPI 2 toolkit bridge at-spi2-core: at-spi2-core/2.34.0 Assistive Technology Service Provider Interface. atk: atk/2.34.1 ATK provides the set of accessibility interfaces that are implemented by other toolkits and applications. Using the ATK interfaces, accessibility tools have full access to view and control running applications. atlas: atlas/3.10.2-lapack-3.6.1 ATLAS (Automatically Tuned Linear Algebra Software) is the application of the AEOS (Automated Empirical Optimization of Software) paradigm, with the present emphasis on the Basic Linear Algebra Subprograms (BLAS), a widely used, performance-critical, linear algebra kernel library. augustus: augustus/3.3 AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences autoconf: autoconf/2.69 Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating system features that the package can use, in the form of M4 macro calls. autodock: autodock/4.2.6 AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. autogrid: autogrid/4.2.6 AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. automake: automake/1.15, automake/1.16.1, automake/1.16.2 Automake: GNU Standards-compliant Makefile generator autotools: autotools/20150215, autotools/20180311, autotools/20200321 This bundle collect the standard GNU build tools: Autoconf, Automake and libtool awscli: awscli/1.16.290-python-3.7.4 Universal Command Line Environment for AWS bam2fastx: bam2fastx/1.3.1 Conversion of PacBio BAM files into gzipped fasta and fastq files, including splitting of barcoded data bamm: bamm/2.5.0 BAMM is oriented entirely towards detecting and quantifying heterogeneity in evolutionary rates. It uses reversible jump Markov chain Monte Carlo to automatically explore a vast universe of candidate models of lineage diversification and trait evolution. bamtools: bamtools/2.5.1 BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files. barrnap: barrnap/0.9 Barrnap (BAsic Rapid Ribosomal RNA Predictor) predicts the location of ribosomal RNA genes in genomes. basemap: basemap/1.2.1-python-3.7.4 The matplotlib basemap toolkit is a library for plotting 2D data on maps in Python bazel: bazel/0.26.1, bazel/0.29.1, bazel/1.1.0, bazel/3.4.1 Bazel is a build tool that builds code quickly and reliably. It is used to build the majority of Google's software. bbmap: bbmap/38.76 BBMap short read aligner, and other bioinformatic tools. bcftools: bcftools/1.9, bcftools/1.12 Samtools is a suite of programs for interacting with high-throughput sequencing data. BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants beagle-lib: beagle-lib/3.0.2 beagle-lib is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. beast: beast/1.10.4, beast/2.5.1, beast/2.6.2, beast/2.6.3 BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. bedtools: bedtools/2.27.1 The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. berkeleyupc: berkeleyupc/2020.4.0 Unified Parallel C (UPC) is an extension of the C programming language designed for high performance computing on large-scale parallel machines.The language provides a uniform programming model for both shared and distributed memory hardware. The programmer is presented with a single shared, partitioned address space, where variables may be directly read and written by any processor, but each variable is physically associated with a single processor. UPC uses a Single Program Multiple Data (SPMD) model of computation in which the amount of parallelism is fixed at program startup time, typically with a single thread of execution per processor. berkeleyupc++: berkeleyupc++/2020.3.2 Unified Parallel C (UPC) is an extension of the C programming language designed for high performance computing on large-scale parallel machines.The language provides a uniform programming model for both shared and distributed memory hardware. The programmer is presented with a single shared, partitioned address space, where variables may be directly read and written by any processor, but each variable is physically associated with a single processor. UPC uses a Single Program Multiple Data (SPMD) model of computation in which the amount of parallelism is fixed at program startup time, typically with a single thread of execution per processor. berkeleyupc-translator: berkeleyupc-translator/2.28.0 Unified Parallel C (UPC) is an extension of the C programming language designed for high performance computing on large-scale parallel machines.The language provides a uniform programming model for both shared and distributed memory hardware. The programmer is presented with a single shared, partitioned address space, where variables may be directly read and written by any processor, but each variable is physically associated with a single processor. UPC uses a Single Program Multiple Data (SPMD) model of computation in which the amount of parallelism is fixed at program startup time, typically with a single thread of execution per processor. berokka: berokka/0.2.3 Trim, circularise and orient long read bacterial genome assemblies bgen: bgen/1.1.7, bgen/3.0.2 This repository contains a reference implementation of the BGEN format, written in C++. The library can be used as the basis for BGEN support in other software, or as a reference for developers writing their own implementations of the BGEN format. binutils: binutils/2.27, binutils/2.32, binutils/2.34, binutils/2.35 binutils: GNU binary utilities bio-db-hts: bio-db-hts/3.01-perl-5.30.0 Read files using HTSlib including BAM/CRAM, Tabix and BCF database files biobambam2: biobambam2/2.0.87 Tools for processing BAM files biom-format: biom-format/2.1.6-python-2.7.16 The BIOM file format (canonically pronounced biome) is designed to be a general-use format for representing biological sample by observation contingency tables. bioperl: bioperl/1.6.924-perl-5.30.0 Bioperl is the product of a community effort to produce Perl code which is useful in biology. Examples include Sequence objects, Alignment objects and database searching objects. biopython: biopython/1.74, biopython/1.75-python-2.7.16, biopython/1.75-python-3.7.4, biopython/1.78-python-3.7.4 Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics. bismark: bismark/0.22.3 A tool to map bisulfite converted sequence reads and determine cytosine methylation states bison: bison/3.0.4, bison/3.0.5, bison/3.3.2, bison/3.5.3, bison/3.6.1, bison/3.7.1 Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables. blast: blast/2.10.0-linux_x86_64 Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. blast+: blast+/2.2.31, blast+/2.9.0 Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. blat: blat/3.5 BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more. blis: blis/0.6.0 BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries. bokeh: bokeh/1.4.0-python-3.7.4 Statistical and novel interactive HTML plots for Python bonito: bonito/0.3.1-python-3.7.4 Convolution Basecaller for Oxford Nanopore Reads boost: boost/1.64.0, boost/1.68.0-python-3.7.4, boost/1.71.0-python-2.7.16, boost/1.71.0 Boost provides free peer-reviewed portable C++ source libraries. boost.python: boost.python/1.71.0-python-2.7.16, boost.python/1.71.0-python-3.7.4 Boost.Python is a C++ library which enables seamless interoperability between C++ and the Python programming language. botocore: botocore/1.16.25-python-3.7.4 Universal Command Line Interface for Amazon Web Services bowtie: bowtie/1.2.3 Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome. bowtie2: bowtie2/2.3.5.1 Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes. bsddb3: bsddb3/6.2.6 bsddb3 is a nearly complete Python binding of the Oracle/Sleepycat C API for the Database Environment, Database, Cursor, Log Cursor, Sequence and Transaction objects. bubblewrap: bubblewrap/0.4.0 Bubblewrap could be viewed as setuid implementation of a subset of user namespaces. Emphasis on subset - specifically relevant to the above CVE, bubblewrap does not allow control over iptables. The original bubblewrap code existed before user namespaces - it inherits code from xdg-app helper which in turn distantly derives from linux-user-chroot. busco: busco/4.0.5-python-3.7.4, busco/5.0.0-python-3.7.4 BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs bwa: bwa/0.7.17 Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. bwa-meth: bwa-meth/0.2.2 Fast and accurante alignment of BS-Seq reads. bzip2: bzip2/1.0.8 bzip2 is a freely available, patent free, high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression. cafexp: cafexp/5.0b2 The purpose of CAFE is to analyze changes in gene family size in a way that accounts for phylogenetic history and provides a statistical foundation for evolutionary inferences. cairo: cairo/1.16.0 Cairo is a 2D graphics library with support for multiple output devices. Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB camisim: camisim/1.2-beta-python-2.7.16 CAMISIM is a software to model abundance distributions of microbial communities and to simulate corresponding shotgun metagenome datasets. canu: canu/1.8-perl-5.30.0, canu/1.9-java-11.0.2, canu/2.0-java-11.0.2 Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing capnproto: capnproto/0.7.0 Cap’n Proto is an insanely fast data interchange format and capability-based RPC system. cd-hit: cd-hit/4.8.1 CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences. cdo: cdo/1.9.8 CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data. cellranger: cellranger/3.1.0 Cell Ranger is a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis. centrifuge: centrifuge/1.0.3 Classifier for metagenomic sequences cfitsio: cfitsio/3.47 CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format. cftime: cftime/1.0.1-python-3.7.4 Time-handling functionality from netcdf4-python cgal: cgal/4.14.1-python-2.7.16-qt4, cgal/4.14.1-python-2.7.16, cgal/4.14.1-python-3.7.4 The goal of the CGAL Open Source Project is to provide easy access to efficient and reliable geometric algorithms in the form of a C++ library. cgpbigwig: cgpbigwig/1.5.0 cgpvcf: cgpvcf/2.0.4 cgpVcf contains a set of common perl utilities for generating consistent Vcf headers. charls: charls/2.1.0 CharLS is a C++ implementation of the JPEG-LS standard for lossless and near-lossless image compression and decompression. JPEG-LS is a low-complexity image compression standard that matches JPEG 2000 compression ratios. chaste: chaste/2019.1 Chaste (Cancer, Heart and Soft Tissue Environment) is a general purpose simulation package aimed at multi-scale, computationally demanding problems arising in biology and physiology. Current functionality includes tissue and cell level electrophysiology, discrete tissue modelling, and soft tissue modelling. checkm: checkm/1.1.2-python-3.7.4 CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. checkm-genome: checkm-genome/1.1.3-python-3.7.4 Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes. checkmate: checkmate/2.0.26 CheckMATE (Check Models At Terascale Energies) is a program package which accepts simulated event files in many formats for any given model. chimera: chimera/1.14-linux_x86_64 UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. circos: circos/0.69-6-perl-5.30.0 Circos is a software package for visualizing data and information. It visualizes data in a circular layout - this makes Circos ideal for exploring relationships between objects or positions. cistem: cistem/1.0.0-beta cisTEM is user-friendly software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them. clang: clang/10.0.0 C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC. clapack: clapack/3.2.1 C version of LAPACK clhep: clhep/2.4.1.3 The CLHEP project is intended to be a set of HEP-specific foundation and utility classes such as random generators, physics vectors, geometry and linear algebra. CLHEP is structured in a set of packages independent of any external package. clisp: clisp/2.49 Common Lisp is a high-level, general-purpose, object-oriented, dynamic, functional programming language. clonalframeml: clonalframeml/1.12 Efficient Inference of Recombination in Whole Bacterial Genomes clustal-omega: clustal-omega/1.2.4 Clustal Omega is the latest addition to the Clustal family. It offers a significant increase in scalability over previous versions, allowing hundreds of thousands of sequences to be aligned in only a few hours. It will also make use of multiple processors, where present. In addition, the quality of alignments is superior to previous versions, as measured by a range of popular benchmarks. cmake: cmake/3.16.1, cmake/3.16.4, cmake/3.18.4 CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software. comsol: comsol/5.5, comsol/5.6 COMSOL is a cross-platform finite element analysis, solver adn multipyhsics simulation software connectomeworkbench: connectomeworkbench/1.4.2 Connectome Workbench is an open source, freely available visualization and discovery tool used to map neuroimaging data, especially data generated by the Human Connectome Project. core/easybuild: core/easybuild/4.3.1 EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way. coreutils: coreutils/8.29 The GNU Core Utilities are the basic file, shell and text manipulation utilities of the GNU operating system. These are the core utilities which are expected to exist on every operating system. cplex: cplex/12.8 IBM ILOG CPLEX Optimizer's mathematical programming technology enables analytical decision support for improving efficiency, reducing costs, and increasing profitability. cpmd: cpmd/4.3 The CPMD code is a parallelized plane wave / pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics. cromwell: cromwell/51-java-11.0.2 Cromwell is a Workflow Management System geared towards scientific workflows. cuda: cuda/8.0.61, cuda/10.1.243, cuda/10.2.89, cuda/11.1.1 CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs. cudacore: cudacore/11.1.1 CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs. cudnn: cudnn/7.6.4.38-cuda-10.1.243, cudnn/7.6.4.38, cudnn/8.0.4.30-cuda-11.1.1 The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks. cufflinks: cufflinks/20190706 Transcript assembly, differential expression, and differential regulation for RNA-Seq cupy: cupy/8.1.0-python-3.7.4 CuPy is an open-source array library accelerated with NVIDIA CUDA. curl: curl/7.66.0, curl/7.69.1, curl/7.72.0 libcurl is a free and easy-to-use client-side URL transfer library, supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling and more. cutadapt: cutadapt/2.8-python-3.7.4 Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. cython: cython/0.27.3-python-2.7.16 Cython is an optimising static compiler for both the Python programming language and the extended Cython programming language (based on Pyrex). cytoscape: cytoscape/3.8.1 Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data. d4: d4/0.1.16 We sought to improve on existing formats such as BigWig and compressed BED files by creating the Dense Depth Data Dump (D4) format and tool suite. The D4 format is adaptive in that it profiles a random sample of aligned sequence depth from the input BAM or CRAM file to determine an optimal encoding that minimizes file size, while also enabling fast data access. dadi: dadi/2.1.0-python-3.7.4 ∂a∂i implements methods for demographic history and selection inference from genetic data, based on diffusion approximations to the allele frequency spectrum. darknet: darknet/20190209 Darknet is an open source neural network framework written in C and CUDA. dask: dask/2.8.0-python-3.7.4 Dask natively scales Python. Dask provides advanced parallelism for analytics, enabling performance at scale for the tools you love. datamash: datamash/1.6, datamash/1.7 GNU datamash is a command-line program which performs basic numeric, textual and statistical operations on input textual data files. dateutils: dateutils/0.4.7 Dateutils are a bunch of tools that revolve around fiddling with dates and times on the command line with a strong focus on use cases that arise when dealing with large amounts of financial data. db: db/6.2.23, db/18.1.40 Berkeley DB enables the development of custom data management solutions, without the overhead traditionally associated with such custom projects. db_file: db_file/1.835-perl-5.30.0 Perl5 access to Berkeley DB version 1.x. dbd-mysql: dbd-mysql/4.050-perl-5.30.0 Perl binding for MySQL dbus: dbus/1.13.12 D-Bus is a message bus system, a simple way for applications to talk to one another. In addition to interprocess communication, D-Bus helps coordinate process lifecycle; it makes it simple and reliable to code a "single instance" application or daemon, and to launch applications and daemons on demand when their services are needed. dbus-glib: dbus-glib/0.110 D-Bus is a message bus system, a simple way for applications to talk to one another. dcm2niix: dcm2niix/1.0.20200331 dcm2niix is a designed to convert neuroimaging data from the DICOM format to the NIfTI format. dcmtk: dcmtk/3.6.5 DCMTK is a collection of libraries and applications implementing large parts the DICOM standard. It includes software for examining, constructing and converting DICOM image files, handling offline media, sending and receiving images over a network connection, as well as demonstrative image storage and worklist servers. deepsqueak: deepsqueak/2.6.1 DeepSqueak is a fully graphical MATLAB package for detecting and classifying rodent ultrasonic vocalizations (USVs). DeepSqueak provides a fully automated pipeline for USV detection, classification, and analysis: deeptools: deeptools/3.3.1-python-3.7.4 deepTools is a suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq. defects4j: defects4j/1.5.0, defects4j/2.0.0 Defects4J is a collection of reproducible bugs and a supporting infrastructure with the goal of advancing software engineering research. delphes: delphes/3.4.2 Delphes is a C++ framework, performing a fast multipurpose detector response simulation. dendropy: dendropy/4.4.0 A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters. diamond: diamond/0.9.30 DIAMOND is a sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000. dotnet-sdk: dotnet-sdk/2.2.203-linux-x64, dotnet-sdk/3.1.300-linux-x64 .NET is a free, cross-platform, open source developer platform for building many different types of applications. double-conversion: double-conversion/3.1.4 Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles. doxygen: doxygen/1.8.16 Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D. duck: duck/7.4.4.33273 duck is a WebDAV client. dynare: dynare/4.6.1 Dynare is a software platform for handling a wide class of economic models, in particular dynamic stochastic general equilibrium (DSGE) and overlapping generations (OLG) models. easybuild: easybuild/4.0.1 EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way. easyspin: easyspin/5.2.28-matlab-2020a EasySpin is a MATLAB toolbox for simulating and fitting a wide range of Electron Paramagnetic Resonance (EPR) spectra. It supplements the numerical and visualization power of MATLAB with the best computational methods devised by EPR spectroscopists. eazy-photoz: eazy-photoz/20201002 EAZY is a photometric redshift code designed to produce high-quality redshifts for situations where complete spectroscopic calibration samples are not available. eccodes: eccodes/2.15.0 ecCodes is a package developed by ECMWF which provides an application programming interface and a set of tools for decoding and encoding messages in the following formats: WMO FM-92 GRIB edition 1 and edition 2, WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated header (only decoding). eggnog-mapper: eggnog-mapper/1.0.3-python-3.7.4 eggnog-mapper is a tool for fast functional annotation of novel sequences (genes or proteins) using precomputed eggNOG-based orthology assignments eigen: eigen/3.3.7, eigen/3.3.8 Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms. eigensoft: eigensoft/7.2.1 The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker’s variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes. elpa: elpa/2019.11.001 Eigenvalue SoLvers for Petaflop-Applications . emacs: emacs/26.3 GNU Emacs is an extensible, customizable text editor--and more. At its core is an interpreter for Emacs Lisp, a dialect of the Lisp programming language with extensions to support text editing. emboss: emboss/6.6.0-java-11.0.2 EMBOSS is 'The European Molecular Biology Open Software Suite' . EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. enabrowsertool: enabrowsertool/1.5.4-python-3.7.4, enabrowsertool/1.6-python-3.7.4 enaBrowserTools is a set of scripts that interface with the ENA web services to download data from ENA easily, without any knowledge of scripting required. esmf: esmf/8.0.0 The Earth System Modeling Framework (ESMF) is software for building and coupling weather, climate, and related models. exiftool: exiftool/12.00 Perl module (Image::ExifTool) and program (exiftool) to read EXIF information from images exiv2: exiv2/0.27.3 Exiv2 is a C++ library and a command line utility to read, write, delete and modify Exif, IPTC, XMP and ICC image metadata. expat: expat/2.2.7, expat/2.2.9 Expat is an XML parser library written in C. It is a stream-oriented parser in which an application registers handlers for things the parser might find in the XML document (like start tags) f5c: f5c/v0.4, f5c/v0.5 f5c is an optimised re-implementation of the call-methylation and eventalign modules in Nanopolish. fasta: fasta/36.3.8g The FASTA programs find regions of local or global (new) similarity between protein or DNA sequences, either by searching Protein or DNA databases, or by identifying local duplications within a sequence. fastaindex: fastaindex/0.11rc7-python-2.7.16 FastA index (.fai) handler compatible with samtools faidx fastani: fastani/1.1, fastani/1.2 FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies. fastgear: fastgear/20161216 Inference of recent and ancestral recombination between divergent lineages in bacteria. fastp: fastp/0.20.0 A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. fastq-pair: fastq-pair/1.0 Match up paired end fastq files quickly and efficiently. fastq-screen: fastq-screen/0.14.1-perl-5.30.0 FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect. fastqc: fastqc/0.11.9-java-11.0.2 FastQC is a quality control application for high throughput sequence data. It reads in sequence data in a variety of formats and can either provide an interactive application to review the results of several different QC checks, or create an HTML based report which can be integrated into a pipeline. fastspar: fastspar/1.0.0 FastSpar is a C++ implementation of the SparCC algorithm which is up to several thousand times faster than the original Python2 release and uses much less memory. faststructure: faststructure/1.0-python-2.7.16 fastStructure is a fast algorithm for inferring population structure from large SNP genotype data. It is based on a variational Bayesian framework for posterior inference and is written in Python2.x. fasttree: fasttree/2.1.10 FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory. fds: fds/6.7.1, fds/6.7.5 Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and heat transport from fires. ffc: ffc/2018.1.0-python-3.7.4 The FEniCS Form Compiler (FFC) is a compiler for finite element variational forms. ffmpeg: ffmpeg/4.2.1, ffmpeg/4.3.1 A complete, cross-platform solution to record, convert and stream audio and video. fftw: fftw/3.3.8 FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data. fiat: fiat/2018.1.0-python-3.7.4 The FInite element Automatic Tabulator (FIAT) supports generation of arbitrary order instances of the Lagrange elements on lines, triangles, and tetrahedra. It is also capable of generating arbitrary order instances of Jacobi-type quadrature rules on the same element shapes. fiji: fiji/2.0-java-11.0.2 Fiji is an image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis. file: file/5.35 The file command is 'a file type guesser', that is, a command-line tool that tells you in words what kind of data a file contains. filtlong: filtlong/0.2.0 Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter flash: flash/1.2.11, flash/2.2.00 FLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate software tool to merge paired-end reads from next-generation sequencing experiments. FLASH is designed to merge pairs of reads when the original DNA fragments are shorter than twice the length of reads. The resulting longer reads can significantly improve genome assemblies. They can also improve transcriptome assembly when FLASH is used to merge RNA-seq data. flatbuffers: flatbuffers/1.12.0 FlatBuffers: Memory Efficient Serialization Library flex: flex/2.6.0, flex/2.6.3, flex/2.6.4 Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text. fltk: fltk/1.3.4, fltk/1.3.5 FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its built-in GLUT emulation. flye: flye/2.6-python-3.7.4, flye/2.8-python-3.7.4 Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies. fontconfig: fontconfig/2.13.1, fontconfig/2.13.92 Fontconfig is a library designed to provide system-wide font configuration, customization and application access. foss: foss/2019b, foss/2020b GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK. fosscuda: fosscuda/2019b, fosscuda/2020b GCC based compiler toolchain __with CUDA support__, and including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK. fraggenescan: fraggenescan/1.31 FragGeneScan is an application for finding (fragmented) genes in short reads. freebayes: freebayes/1.3.2-java-11.0.2 Bayesian haplotype-based polymorphism discovery and genotyping. freeglut: freeglut/3.0.0-mesa18, freeglut/3.0.0-mesa19, freeglut/3.0.0, freeglut/3.2.1 freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library. freesurfer: freesurfer/6.0.1-centos6_x86_64, freesurfer/7.1.0-centos7_x86_64, freesurfer/7.1.1-centos7_x86_64 FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data. FreeSurfer contains a fully automatic structural imaging stream for processing cross sectional and longitudinal data. freetype: freetype/2.10.1, freetype/2.10.3 FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display servers, font conversion tools, text image generation tools, and many other products as well. freexl: freexl/1.0.5 FreeXL is an open source library to extract valid data from within an Excel (.xls) spreadsheet. fribidi: fribidi/1.0.5, fribidi/1.0.10 The Free Implementation of the Unicode Bidirectional Algorithm. fsl: fsl/6.0.1-python-3.7.4, fsl/6.0.3-python-3.7.4 FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. fsleyes: fsleyes/0.32.3, fsleyes/0.34.2 FSLeyes, the FSL image viewer. ftgl: ftgl/2.1.3-rc5 FTGL is a free open source library to enable developers to use arbitrary fonts in their OpenGL (www.opengl.org) applications. g2clib: g2clib/1.6.0 Library contains GRIB2 encoder/decoder ('C' version). g2lib: g2lib/3.1.0 Library contains GRIB2 encoder/decoder and search/indexing routines. gapcloser: gapcloser/1.12-r6 GapCloser is designed to close the gaps emerging during the scaffolding process by SOAPdenovo or other assembler, using the abundant pair relationships of short reads. gatk: gatk/4.1.0.0-python-3.7.4, gatk/4.1.4.1-python-3.7.4 The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. gaussian: gaussian/g16c01 Gaussian provides electronic structure modeling. gc: gc/7.6.12 The Boehm-Demers-Weiser conservative garbage collector can be used as a garbage collecting replacement for C malloc or C++ new. gcc: gcc/8.2.0-2.31.1, gcc/8.3.0, gcc/8.3.0-2.32, gcc/9.2.0, gcc/10.1.0, gcc/10.2.0 The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...). gcccore: gcccore/6.3.0, gcccore/8.3.0, gcccore/9.2.0, gcccore/10.1.0, gcccore/10.2.0 The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...). gcccuda: gcccuda/2019b, gcccuda/2020b GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit. gconf: gconf/3.2.6 GConf is a system for storing application preferences. It is intended for user preferences; not configuration of something like Apache, or arbitrary data storage. gd: gd/2.69-perl-5.30.0 GD.pm - Interface to Gd Graphics Library gdal: gdal/3.0.2-python-3.7.4 GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for data translation and processing. gdb: gdb/9.1-python-3.7.4 The GNU Project Debugger gdk-pixbuf: gdk-pixbuf/2.38.2 The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it was distributed as part of GTK+ 2 but it was split off into a separate package in preparation for the change to GTK+ 3. gdrcopy: gdrcopy/2.0 A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology. geant4: geant4/10.6 Geant4 is a toolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science. gencore: gencore/0.13.0 An efficient tool to remove sequencing duplications and eliminate sequencing errors by generating consensus reads. gensim: gensim/0.13.2-python-2.7.16 Gensim is a Python library for topic modelling, document indexing and similarity retrieval with large corpora. geos: geos/3.7.2-python-3.7.4, geos/3.8.0-python-3.7.4 GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS) gettext: gettext/0.19.8.1, gettext/0.20.1, gettext/0.21 GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation gffcompare: gffcompare/0.12.2 GffCompare compares and evaluates the accuracy of RNA-Seq transcript assemblers (Cufflinks, Stringtie). gflags: gflags/2.2.2 The gflags package contains a C++ library that implements commandline flags processing. It includes built-in support for standard types such as string and the ability to define flags in the source file in which they are used. ghostscript: ghostscript/9.27, ghostscript/9.50 Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to different targets. It used to be part of the cups printing stack, but is no longer used for that. giflib: giflib/5.1.4, giflib/5.2.1 giflib is a library for reading and writing gif images. It is API and ABI compatible with libungif which was in wide use while the LZW compression algorithm was patented. git: git/2.23.0-nodocs, git/2.23.0 Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency. gitpython: gitpython/2.1.11 GitPython is a python library used to interact with Git repositories gl2ps: gl2ps/1.4.0-mesa18, gl2ps/1.4.0-mesa19, gl2ps/1.4.0 GL2PS: an OpenGL to PostScript printing library glib: glib/2.62.0 GLib is one of the base libraries of the GTK+ project glibmm: glibmm/2.49.7 C++ bindings for Glib glm: glm/0.9.9.0 OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics software based on the OpenGL Shading Language (GLSL) specifications. glog: glog/0.3.5, glog/0.4.0 A C++ implementation of the Google logging module. glpk: glpk/4.65 The GLPK (GNU Linear Programming Kit) package is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems. It is a set of routines written in ANSI C and organized in the form of a callable library. gmap-gsnap: gmap-gsnap/2016-11-07 GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences GSNAP: Genomic Short-read Nucleotide Alignment Program gmp: gmp/6.1.2, gmp/6.2.0 GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers. gmsh: gmsh/4.2.2-python-3.7.4 Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor. gnucobol: gnucobol/3.0-rc1 GnuCOBOL (formerly OpenCOBOL) is a free COBOL compiler. cobc translates COBOL source to executable using intermediate C, designated C compiler and linker. gnuplot: gnuplot/5.2.6, gnuplot/5.2.8 Portable interactive, function plotting utility gnutls: gnutls/3.6.15 GnuTLS is a secure communications library implementing the SSL, TLS and DTLS protocols and technologies around them. It provides a simple C language application programming interface (API) to access the secure communications protocols as well as APIs to parse and write X.509, PKCS #12, OpenPGP and other required structures. It is aimed to be portable and efficient with focus on security and interoperability. go: go/1.14.1 Go is an open source programming language that makes it easy to build simple, reliable, and efficient software. gobject-introspection: gobject-introspection/1.60.1-python-3.7.4, gobject-introspection/1.63.1-python-3.7.4 GObject introspection is a middleware layer between C libraries (using GObject) and language bindings. The C library can be scanned at compile time and generate a metadata file, in addition to the actual native C library. Then at runtime, language bindings can read this metadata and automatically provide bindings to call into the C library. gompi: gompi/2019b, gompi/2020b GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support. gompic: gompic/2019b, gompic/2020b GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, including OpenMPI for MPI support with CUDA features enabled. googletest: googletest/1.10.0 Google's framework for writing C++ tests on a variety of platforms gperf: gperf/3.1 GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single string comparison only. gperftools: gperftools/2.7.90 gperftools are for use by developers so that they can create more robust applications. Especially of use to those developing multi-threaded applications in C++ with templates. Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler. graphicsmagick: graphicsmagick/1.3.31, graphicsmagick/1.3.34 GraphicsMagick is the swiss army knife of image processing. grass: grass/7.8.3-python-3.7.4 The Geographic Resources Analysis Support System - used for geospatial data management and analysis, image processing, graphics and maps production, spatial modeling, and visualization groff: groff/1.22.4 Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands and produces formatted output. grom: grom/1.0.3 GROM is optimally designed for whole genome sequencing (Illumina paired-end or single-end) data aligned with BWA mem and has been used to analyze exome and RNA-seq data. GROM analysis is limited to SNVs and indels for exome and RNA-seq data. gromacs: gromacs/2018.4-plumed-2.5.0, gromacs/2020, gromacs/2020.4-plumed-2.6.2 GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. This is a GPU enabled build, containing both MPI and threadMPI binaries. gsl: gsl/2.5, gsl/2.6 The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. gst-plugins-base: gst-plugins-base/1.16.0 GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio (mixing) and video (non-linear editing) processing. gstreamer: gstreamer/1.16.0 GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio (mixing) and video (non-linear editing) processing. gtdb-tk: gtdb-tk/0.3.2-python-2.7.16 A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes. gtk+: gtk+/3.24.8, gtk+/3.24.13 GTK+ is the primary library used to construct user interfaces in GNOME. It provides all the user interface controls, or widgets, used in a common graphical application. Its object-oriented API allows you to construct user interfaces without dealing with the low-level details of drawing and device interaction. gts: gts/0.7.6 GTS stands for the GNU Triangulated Surface Library. It is an Open Source Free Software Library intended to provide a set of useful functions to deal with 3D surfaces meshed with interconnected triangles. gubbins: gubbins/2.4.0 Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. Simulations demonstrate the algorithm generates highly accurate reconstructions under realistic models of short-term bacterial evolution, and can be run in only a few hours on alignments of hundreds of bacterial genome sequences. guile: guile/1.8.8, guile/3.0.4 Guile is a programming language, designed to help programmers create flexible applications that can be extended by users or other programmers with plug-ins, modules, or scripts. guppy: guppy/3.6.1 Guppy software supports MinIT and MinION instruments from Nanopore Technologies gurobi: gurobi/9.0.0, gurobi/9.0.3 The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern architectures and multi-core processors, using the most advanced implementations of the latest algorithms. gzip: gzip/1.10 gzip (GNU zip) is a popular data compression program as a replacement for compress h5py: h5py/2.9.0, h5py/2.10.0-python-3.7.4 HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data. harfbuzz: harfbuzz/2.4.0, harfbuzz/2.6.4 HarfBuzz is an OpenType text shaping engine. hdbscan: hdbscan/0.8.26-python-3.7.4 Hierarchical Density-Based Spatial Clustering of Applications with Noise. Performs DBSCAN over varying epsilon values and integrates the result to find a clustering that gives the best stability over epsilon. This allows HDBSCAN to find clusters of varying densities (unlike DBSCAN), and be more robust to parameter selection. hdf: hdf/4.2.14 HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines. hdf5: hdf5/1.8.12, hdf5/1.10.5-nompi, hdf5/1.10.5 HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data. heaptrack: heaptrack/1.2.0 A heap memory profiler for Linux. help2man: help2man/1.47.4, help2man/1.47.8, help2man/1.47.10, help2man/1.47.15, help2man/1.47.16 help2man produces simple manual pages from the '--help' and '--version' output of other commands. hepmc2: hepmc2/2.06.10 The HepMC package is an object oriented, C++ event record for High Energy Physics Monte Carlo generators and simulation. The original code was written by M. Dobbs and J.B. Hansen (Comput. Phys. Commun. 134 (2001) 41). Since the first implementation, the package has undergone several modifications and in particular, the latest HepMC3 series is a completely new re-write using currently available C++11 techniques. hisat2: hisat2/2.1.0 HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome). hivtrace: hivtrace/0.6.2-python-3.7.4 HIV-TRACE is an application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database. hmmcopyutils: hmmcopyutils/20170719 This repo provides tools for extracting read counts and gc and mappability statistics in preparation for running HMMCopy. hmmer: hmmer/3.2.1, hmmer/3.3.1, hmmer/3.3.2 HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST. hmmer2: hmmer2/2.3.2 HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. horovod: horovod/0.18.1-python-3.7.4, horovod/0.18.2-tensorflow-1.15.0-python-3.7.4 Horovod is a distributed training framework for TensorFlow. htseq: htseq/0.11.2-python-2.7.16, htseq/0.11.2-python-3.7.4 HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments. htslib: htslib/1.9, htslib/1.10.2, htslib/1.12 A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix hwloc: hwloc/1.11.12, hwloc/2.0.3, hwloc/2.2.0 The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently. hyphy: hyphy/2.5.1, hyphy/2.5.17 HyPhy (Hypothesis Testing using Phylogenies) is an open-source software package for the analysis of genetic sequences (in particular the inference of natural selection) using techniques in phylogenetics, molecular evolution, and machine learning hypo: hypo/1.0.3-python-3.7.4 HyPo: Super Fast & Accurate Polisher for Long Read Genome Assemblies hypothesis: hypothesis/4.44.2-python-3.7.4, hypothesis/5.41.5-python-3.8.6 Hypothesis is an advanced testing library for Python. It lets you write tests which are parametrized by a source of examples, and then generates simple and comprehensible examples that make your tests fail. This lets you find more bugs in your code with less work. hypre: hypre/2.18.2 Hypre is a library for solving large, sparse linear systems of equations on massively parallel computers. The problems of interest arise in the simulation codes being developed at LLNL and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences. icc: icc/2017.2.174-gcc-6.3.0-2.27, icc/2019.5.281-gcc-8.3.0-2.32 C and C++ compiler from Intel iccifort: iccifort/2017.2.174-gcc-6.3.0-2.27, iccifort/2019.5.281-gcc-8.3.0-2.32 Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL iccifortcuda: iccifortcuda/2019.5.281-gcc-8.3.0-2.32 Intel C, C++ & Fortran compilers with CUDA toolkit icu: icu/64.2, icu/65.1 ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications. idba-ud: idba-ud/1.1.3 IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm. IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth contigs are removed iteratively with cutoff threshold from low to high to reduce the errors in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD can iterate k value of de Bruijn graph to a very large value with less gaps and less branches to form long contigs in both low-depth and high-depth regions. ifort: ifort/2017.2.174-gcc-6.3.0-2.27, ifort/2019.5.281-gcc-8.3.0-2.32 Fortran compiler from Intel igv: igv/2.8.0-java-11.0.2 This package contains command line utilities for preprocessing, computing feature count density (coverage), sorting, and indexing data files. imagemagick: imagemagick/7.0.8-46, imagemagick/7.0.9-5 ImageMagick is a software suite to create, edit, compose, or convert bitmap images imkl: imkl/2017.2.174, imkl/2019.5.281 Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more. inputproto: inputproto/2.3.2 X.org InputProto protocol headers. intarna: intarna/3.2.0-python-3.7.4 Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites intelpython: intelpython/2.7.16-2019.5.098, intelpython/3.6.8-2019.2.066 Intel Distribution for Python. Powered by Anaconda. Accelerating Python* performance on modern architectures from Intel. intltool: intltool/0.51.0 intltool is a set of tools to centralize translation of many different file formats using GNU gettext-compatible PO files. iomkl: iomkl/2017.02, iomkl/2019.05 Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI. iomklc: iomklc/2019.05 Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI. iompi: iompi/2017.02, iompi/2019.05 Intel C/C++ and Fortran compilers, alongside Open MPI. iompic: iompic/2019.05 Intel C/C++ and Fortran compilers, alongside Intel MPI and CUDA. ipython: ipython/5.8.0-python-2.7.16, ipython/7.9.0-python-3.7.4 IPython provides a rich architecture for interactive computing with: Powerful interactive shells (terminal and Qt-based). A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. Support for interactive data visualization and use of GUI toolkits. Flexible, embeddable interpreters to load into your own projects. Easy to use, high performance tools for parallel computing. iq-tree: iq-tree/1.6.12, iq-tree/2.0.6 Efficient phylogenomic software by maximum likelihood jags: jags/4.3.0 JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation jasper: jasper/2.0.14 The JasPer Project is an open-source initiative to provide a free software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard. java: java/1.8.0_241, java/11.0.2 Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers. jchem: jchem/20.15.0-java-1.8.0_241 JChem technology provides sophisticated implementations for chemical representation, search, storage, structural and non-structural data management functions. jellyfish: jellyfish/2.3.0 Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. jemalloc: jemalloc/5.2.1 jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and scalable concurrency support. joe: joe/4.6 JOE is a full featured terminal-based screen editor. jsoncpp: jsoncpp/1.9.3 JsonCpp is a C++ library that allows manipulating JSON values, including serialization and deserialization to and from strings. It can also preserve existing comment in unserialization/serialization steps, making it a convenient format to store user input files. judy: judy/1.0.5 A C library that implements a dynamic array. julia: julia/1.0.4-linux-x86_64, julia/1.1.1-linux-x86_64, julia/1.3.1-linux-x86_64, julia/1.5.1-linux-x86_64 Julia is a high-level, high-performance dynamic programming language for numerical computing junit: junit/4.12-java-1.8.0_241, junit/4.12-java-11.0.2 A programmer-oriented testing framework for Java. jupyter: jupyter/1.0.0-python-3.7.4-sean, jupyter/1.0.0-python-3.7.4 The Jupyter Notebook is an open-source web application that allows you to create and share documents that contain live code, equations, visualizations and narrative text. Uses include: data cleaning and transformation, numerical simulation, statistical modeling, data visualization, machine learning, and much more. kaiju: kaiju/1.7.3-python-3.7.4 Kaiju is a program for sensitive taxonomic classification of high-throughput sequencing reads from metagenomic whole genome sequencing experiments kallisto: kallisto/0.45.1 kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. kat: kat/2.4.2-python-3.7.4 The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra. kbbq: kbbq/20210319 K-mer based base quality score recalibration. kbproto: kbproto/1.0.7 X.org KBProto protocol headers. keras: keras/2.2.4-python-3.7.4 Keras is a minimalist, highly modular neural networks library, written in Python and capable of running on top of either TensorFlow or Theano. kim-api: kim-api/2.1.3 Open Knowledgebase of Interatomic Models. KIM is an API and OpenKIM is a collection of interatomic models (potentials) for atomistic simulations. This is a library that can be used by simulation programs to get access to the models in the OpenKIM database. This EasyBuild only installs the API, the models can be installed with the package openkim-models, or the user can install them manually by running kim-api-collections-management install user MODELNAME or kim-api-collections-management install user OpenKIM to install them all. kmc: kmc/3.1.0, kmc/3.1.2rc1-python-3.7.4 KMC is a disk-based programm for counting k-mers from (possibly gzipped) FASTQ/FASTA files. kraken: kraken/1.1-perl-5.30.0 Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. Kraken aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm. kraken2: kraken2/2.0.8-beta-perl-5.30.0 Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. Kraken aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm. kronatools: kronatools/2.7.1 Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files. lame: lame/3.100 LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL. lammps: lammps/3mar2020-python-3.7.4-kokkos-openmp, lammps/3mar2020-python-3.7.4-kokkos LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality. landis-ii: landis-ii/7.0 The LANDIS-II forest landscape model simulates future forests (both trees and shrubs) at decadal to multi-century time scales and spatial scales spanning hundreds to millions of hectares. lapack: lapack/3.9.0 LAPACK is written in Fortran90 and provides routines for solvin g systems of simultaneous linear equations, least-squares solutions of linear systems of equ ations, eigenvalue problems, and singular value problems. last: last/1066 LAST finds similar regions between sequences. lastz: lastz/1.04.03 LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS sequencing technologies such as Roche 454. leveldb: leveldb/1.22 LevelDB is a fast key-value storage library written at Google that provides an ordered mapping from string keys to string values. libaio: libaio/0.3.111 Asynchronous input/output library that uses the kernels native interface. libarchive: libarchive/3.4.3 Multi-format archive and compression library libbigwig: libbigwig/0.4.4 A C library for handling bigWig files libcerf: libcerf/1.11, libcerf/1.13 libcerf is a self-contained numeric library that provides an efficient and accurate implementation of complex error functions, along with Dawson, Faddeeva, and Voigt functions. libcroco: libcroco/0.6.13 Libcroco is a standalone css2 parsing and manipulation library. libdap: libdap/3.20.4 A C++ SDK which contains an implementation of DAP 2.0 and DAP4.0. This includes both Client- and Server-side support classes. libdrm: libdrm/2.4.99 Direct Rendering Manager runtime library. libdwarf: libdwarf/20190529 The DWARF Debugging Information Format is of interest to programmers working on compilers and debuggers (and anyone interested in reading or writing DWARF information)) libelf: libelf/0.8.13 libelf is a free ELF object file access library libepoxy: libepoxy/1.5.4 Epoxy is a library for handling OpenGL function pointer management for you libevent: libevent/2.1.11, libevent/2.1.12 The libevent API provides a mechanism to execute a callback function when a specific event occurs on a file descriptor or after a timeout has been reached. Furthermore, libevent also support callbacks due to signals or regular timeouts. libfabric: libfabric/1.11.0 Libfabric is a core component of OFI. It is the library that defines and exports the user-space API of OFI, and is typically the only software that applications deal with directly. It works in conjunction with provider libraries, which are often integrated directly into libfabric. libffcall: libffcall/2.2 GNU Libffcall is a collection of four libraries which can be used to build foreign function call interfaces in embedded interpreters libffi: libffi/3.2.1, libffi/3.3 The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run-time. libgcrypt: libgcrypt/1.8.4 Libgpg-error is a small library that defines common error values for all GnuPG components. libgd: libgd/2.2.5 GD is an open source code library for the dynamic creation of images by programmers. libgeotiff: libgeotiff/1.5.1 Library for reading and writing coordinate system information from/to GeoTIFF files libglu: libglu/9.0.0, libglu/9.0.1 The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. libglvnd: libglvnd/1.2.0 libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors. libgpg-error: libgpg-error/1.36 Libgpg-error is a small library that defines common error values for all GnuPG components. libharu: libharu/2.3.0 libHaru is a free, cross platform, open source library for generating PDF files. libiconv: libiconv/1.16 Libiconv converts from one character encoding to another through Unicode conversion libidn: libidn/1.35 GNU Libidn is a fully documented implementation of the Stringprep, Punycode and IDNA specifications. Libidn's purpose is to encode and decode internationalized domain names. libjpeg: libjpeg/9d Libjpeg is a widely used C library for reading and writing JPEG image files. libjpeg-turbo: libjpeg-turbo/2.0.3, libjpeg-turbo/2.0.5 libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding. libmatheval: libmatheval/1.1.11 GNU libmatheval is a library (callable from C and Fortran) to parse and evaluate symbolic expressions input as text. libmaus2: libmaus2/2.0.453 libmaus2 is a collection of data structures and algorithms. libpciaccess: libpciaccess/0.14, libpciaccess/0.16 Generic PCI access library. libpng: libpng/1.6.37 libpng is the official PNG reference library libpsl: libpsl/0.21.0 C library for the Public Suffix List libpthread-stubs: libpthread-stubs/0.4 The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility. libreadline: libreadline/8.0 The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands. librsvg: librsvg/2.48.4 librsvg is a library to render SVG files using cairo. libsigc++: libsigc++/2.10.2 The libsigc++ package implements a typesafe callback system for standard C++. libsigsegv: libsigsegv/2.12 GNU libsigsegv is a library for handling page faults in user mode. libsndfile: libsndfile/1.0.28 Libsndfile is a C library for reading and writing files containing sampled sound (such as MS Windows WAV and the Apple/SGI AIFF format) through one standard library interface. libsodium: libsodium/1.0.18 Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more. libsoup: libsoup/2.66.1 libsoup is an HTTP client/server library for GNOME. It uses GObjects and the glib main loop, to integrate well with GNOME applications, and also has a synchronous API, for use in threaded applications. libspatialite: libspatialite/4.3.0a-python-3.7.4 SpatiaLite is an open source library intended to extend the SQLite core to support fully fledged Spatial SQL capabilities. libtasn1: libtasn1/4.13 Libtasn1 is the ASN.1 library used by GnuTLS, GNU Shishi and some other packages. It was written by Fabio Fiorina, and has been shipped as part of GnuTLS for some time but is now a proper GNU package. libtiff: libtiff/4.0.10, libtiff/4.1.0 tiff: Library and tools for reading and writing TIFF data files libtirpc: libtirpc/1.1.4 Libtirpc is a port of Suns Transport-Independent RPC library to Linux. libtool: libtool/2.4.6 GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface. libunistring: libunistring/0.9.10 This library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard. libunwind: libunwind/1.3.1 The primary goal of libunwind is to define a portable and efficient C programming interface (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain (non-local goto). The API supports both local (same-process) and remote (across-process) operation. As such, the API is useful in a number of applications libuuid: libuuid/1.0.3 Portable uuid C library libwebp: libwebp/1.0.2 WebP is a modern image format that provides superior lossless and lossy compression for images on the web. Using WebP, webmasters and web developers can create smaller, richer images that make the web faster. libx11: libx11/1.6.3 X11 client-side library libxau: libxau/1.0.8 The libXau package contains a library implementing the X11 Authorization Protocol. This is useful for restricting client access to the display. libxc: libxc/4.3.4 Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals. libxcb: libxcb/1.11.1 The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility. libxdmcp: libxdmcp/1.1.2 The libXdmcp package contains a library implementing the X Display Manager Control Protocol. This is useful for allowing clients to interact with the X Display Manager. libxft: libxft/2.3.2 X11 client-side library libxml++: libxml++/2.40.1 libxml++ is a C++ wrapper for the libxml XML parser library. libxml2: libxml2/2.9.9, libxml2/2.9.10 Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform). libxrender: libxrender/0.9.9 X11 client-side library libxslt: libxslt/1.1.33 Libxslt is the XSLT C library developed for the GNOME project (but usable outside of the Gnome platform). libyaml: libyaml/0.2.2, libyaml/0.2.5 LibYAML is a YAML parser and emitter written in C. liggghts: liggghts/3.8.0-python-3.7.4, liggghts/3.8.0 DEM simulation engine, released by DCS Computing GmbH. lighter: lighter/1.1.2 Fast and memory-efficient sequencing error corrector littlecms: littlecms/2.9 Little CMS intends to be an OPEN SOURCE small-footprint color management engine, with special focus on accuracy and performance. llvm: llvm/6.0.0, llvm/8.0.1, llvm/9.0.0 The LLVM Core libraries provide a modern source- and target-independent optimizer, along with code generation support for many popular CPUs (as well as some less common ones!) These libraries are built around a well specified code representation known as the LLVM intermediate representation ("LLVM IR"). The LLVM Core libraries are well documented, and it is particularly easy to invent your own language (or port an existing compiler) to use LLVM as an optimizer and code generator. lmdb: lmdb/0.9.24 LMDB is a fast, memory-efficient database. With memory-mapped files, it has the read performance of a pure in-memory database while retaining the persistence of standard disk-based databases. lpsolve: lpsolve/5.5.2.5 Mixed Integer Linear Programming (MILP) solver lua: lua/5.1.5 Lua is a powerful, fast, lightweight, embeddable scripting language. Lua combines simple procedural syntax with powerful data description constructs based on associative arrays and extensible semantics. Lua is dynamically typed, runs by interpreting bytecode for a register-based virtual machine, and has automatic memory management with incremental garbage collection, making it ideal for configuration, scripting, and rapid prototyping. lz4: lz4/1.9.2 LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core. It features an extremely fast decoder, with speed in multiple GB/s per core. lzo: lzo/2.10 Portable lossless data compression library m4: m4/1.4.17, m4/1.4.18 GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible although it has some extensions (for example, handling more than 9 positional parameters to macros). GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc. macs2: macs2/2.2.7.1-python-3.7.4 MACS captures the influence of genome complexity to evaluate the significance of enriched ChIP regions and MACS improves the spatial resolution of binding sites through combining the information of both sequencing tag position and orientation. MACS can be easily used for ChIP-Seq data alone, or with a control sample with the increase of specificity. madgraph5_amc: madgraph5_amc/2.7.0 MadGraph5_aMC@NLO is a framework that aims at providing all the elements necessary for SM and BSM phenomenology, such as the computations of cross sections, the generation of hard events and their matching with event generators, and the use of a variety of tools relevant to event manipulation and analysis. mafft: mafft/7.310-with-extensions, mafft/7.453-with-extensions MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼10,000 sequences), etc. magma: magma/2.5.1, magma/2.5.4 The MAGMA project aims to develop a dense linear algebra library similar to LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems. makedepend: makedepend/1.0.6 The makedepend package contains a C-preprocessor like utility to determine build-time dependencies. makeinfo: makeinfo/6.7 makeinfo is part of the Texinfo project, the official documentation format of the GNU project. mako: mako/1.1.0 A super-fast templating language that borrows the best ideas from the existing templating languages maple: maple/2018.1 Maple combines the world's most powerful mathematical computation engine with an intuitive, 'clickable' user interface. mariadb: mariadb/10.3.14 MariaDB is an enhanced, drop-in replacement for MySQL. Included engines: myISAM, Aria, InnoDB, RocksDB, TokuDB, OQGraph, Mroonga. mariadb-connector-c: mariadb-connector-c/2.3.7 MariaDB Connector/C is used to connect applications developed in C/C++ to MariaDB and MySQL databases. mash: mash/2.1, mash/2.2 Fast genome and metagenome distance estimation using MinHash masurca: masurca/3.4.2, masurca/4.0.1 MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing only short reads from Illumina sequencing or a mixture of short reads and long reads (Sanger, 454, Pacbio and Nanopore). mathematica: mathematica/12.0.0 Mathematica is a computational software program used in many scientific, engineering, mathematical and computing fields. matio: matio/1.5.12 matio is an C library for reading and writing Matlab MAT files. matlab: matlab/2019a, matlab/2019b, matlab/2020a-update5, matlab/2020a, matlab/2021a MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran. matplotlib: matplotlib/2.2.4-python-2.7.16, matplotlib/2.2.4-python-3.7.4, matplotlib/3.1.1-python-3.7.4, ... matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits. maven: maven/3.6.3 Binary maven install, Apache Maven is a software project management and comprehension tool. Based on the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a central piece of information. maxbin: maxbin/2.2.7-perl-5.30.0 MaxBin is software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. maxima: maxima/5.41.0 Maxima is a system for the manipulation of symbolic and numerical expressions. mcl: mcl/14.137 The MCL algorithm is short for the Markov Cluster Algorithm, a fast and scalable unsupervised cluster algorithm for graphs (also known as networks) based on simulation of (stochastic) flow in graphs. mcr: mcr/r2013a, mcr/r2016a The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed. medaka: medaka/1.1.2 PyTorch Geometric (PyG) is a geometric deep learning extension library for PyTorch. mediaflux-data-mover: mediaflux-data-mover/current mediaflux-data-mover is a data transfer tool for uploading and/or downloading data from a Mediaflux server using a shareable token. megahit: megahit/1.1.4-python-2.7.16, megahit/1.1.4-python-3.7.4, megahit/1.2.9-python-2.7.16 An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph meme: meme/5.1.1-python-3.7.4 The MEME Suite allows you to: * discover motifs using MEME, DREME (DNA only) or GLAM2 on groups of related DNA or protein sequences, * search sequence databases with motifs using MAST, FIMO, MCAST or GLAM2SCAN, * compare a motif to all motifs in a database of motifs, * associate motifs with Gene Ontology terms via their putative target genes, and * analyse motif enrichment using SpaMo or CentriMo. mercurial: mercurial/5.6.1-python-3.7.4 Mercurial is a free, distributed source control management tool. It efficiently handles projects of any size and offers an easy and intuitive interface. mesa: mesa/18.1.1, mesa/19.1.7, mesa/19.2.1 Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics. meson: meson/0.51.2-python-3.7.4, meson/0.55.3-python-3.8.6 Meson is a cross-platform build system designed to be both as fast and as user friendly as possible. metabat: metabat/2.12.1-python-2.7.16 An efficient tool for accurately reconstructing single genomes from complex microbial communities metaeuk: metaeuk/4 MetaEuk is a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic metagenomic contigs. metahipmer: metahipmer/2.0.0 MetaHipMer is a de novo metagenome short-read assembler. Version 2 (MHM2) is written entirely in UPC++ and runs efficiently on both single servers and on multinode supercomputers, where it can scale up to coassemble terabase-sized metagenomes. metaphlan: metaphlan/3.0-python-3.7.4 MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data metavelvet: metavelvet/1.2.02 A short read assember for metagenomics methyldackel: methyldackel/0.5.2 A (mostly) universal methylation extractor for BS-seq experiments. metis: metis/5.1.0 METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes. miniconda2: miniconda2/4.7.10 Miniconda is a free minimal installer for conda. It is a small, bootstrap version of Anaconda that includes only conda, Python, the packages they depend on, and a small number of other useful packages. miniconda3: miniconda3/4.7.10 Miniconda is a free minimal installer for conda. It is a small, bootstrap version of Anaconda that includes only conda, Python, the packages they depend on, and a small number of other useful packages. minimap2: minimap2/2.13, minimap2/2.17 Minimap2 is a fast sequence mapping and alignment program that can find overlaps between long noisy reads, or map long reads or their assemblies to a reference genome optionally with detailed alignment (i.e. CIGAR). At present, it works efficiently with query sequences from a few kilobases to ~100 megabases in length at an error rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limited test data sets, minimap2 is over 20 times faster than most other long-read aligners. It will replace BWA-MEM for long reads and contig alignment. mirdeep2: mirdeep2/0.1.3-python-3.7.4 miRDeep2 is a completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs mlst: mlst/2.16 Scan contig files against traditional PubMLST typing schemes. molmod: molmod/1.4.5-python-3.7.4 MolMod is a Python library with many compoments that are useful to write molecular modeling programs. mono: mono/6.4.0.198 An open source, cross-platform, implementation of C# and the CLR that is binary compatible with Microsoft.NET. mosdepth: mosdepth/0.3.1 fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing. mosek: mosek/9.2 The MOSEK optimization software is designed to solve large-scale mathematical optimization problems. MOSEK main features are listed below. For additional questions, contact our support or browse the online documentation. motif: motif/2.3.8 Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems. It was the standard toolkit for the Common Desktop Environment and thus for Unix. mpfr: mpfr/4.0.2, mpfr/4.1.0 The MPFR library is a C library for multiple-precision floating-point computations with correct rounding. mpi4py: mpi4py/3.0.2-timed-pingpong MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for the Python programming language, allowing any Python program to exploit multiple processors. mpich: mpich/3.3 MPICH v3.x is an open source high-performance MPI 3.0 implementation. It does not support InfiniBand (use MVAPICH2 with InfiniBand devices). mrbayes: mrbayes/3.2.7a, mrbayes/3.2.7 MrBayes is a program for the Bayesian estimation of phylogeny. mrtrix: mrtrix/3.0_rc2-python-2.7.16, mrtrix/3.0.1-python-2.7.16 MRtrix provides a set of tools to perform diffusion-weighted MR white-matter tractography in a manner robust to crossing fibres, using constrained spherical deconvolution (CSD) and probabilistic streamlines. mrtrix3tissue: mrtrix3tissue/5.2.8-python-2.7.16 MRtrix3Tissue is a fork of the MRtrix3 project. It aims to add capabilities for 3-Tissue CSD modelling and analysis to a complete version of the MRtrix3 software. mspc: mspc/4.0.1 The analysis of ChIP-seq samples outputs a number of enriched regions, each indicating a protein-DNA interaction or a specific chromatin modification. Enriched regions (commonly known as "peaks") are called when the read distribution is significantly different from the background and its corresponding significance measure (p-value) is below a user-defined threshold. multiqc: multiqc/1.7-python-3.7.4, multiqc/1.9-python-3.7.4 Aggregate results from bioinformatics analyses across many samples into a single report. MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. multiwell: multiwell/2020 Calculates time dependent concentrations, reaction yields, vibrational distributions, and rate constants as functions of temperature and pressure for multi-well, multi-channel unimolecular reactions systems. multiwfn: multiwfn/3.8 Multiwfn is an extremely powerful program for realizingi electronic wavefunction analysis, which is a key ingredient of quantum chemistry. Multiwfn is free, open-source, high-efficient, very user-friendly and flexible, it supports almost all of the most important wavefunction analysis methods. mummer: mummer/4.0.0beta2 MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. AMOS makes use of it. mumps: mumps/5.2.1-metis A parallel sparse direct solver muscle: muscle/3.8.1551 MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users learn everything they need to know about MUSCLE in a few minutes-only a handful of command-line options are needed to perform common alignment tasks. namd: namd/2.14-mpi, namd/2.14 NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. nanofilt: nanofilt/2.6.0-python-3.7.4 Filtering and trimming of Oxford Nanopore Sequencing data nanoget: nanoget/1.12.1-python-3.7.4, nanoget/1.13.0-python-3.7.4 Functions to extract information from Oxford Nanopore sequencing data and alignments nanomath: nanomath/0.23.1-python-3.7.4 A few simple math function for other Oxford Nanopore processing scripts nanoplot: nanoplot/1.28.4-python-3.7.4, nanoplot/1.30.0-python-3.7.4 Plotting suite for long read sequencing data and alignments nanopolish: nanopolish/0.13.2-mt-python-3.7.4, nanopolish/0.13.2-python-3.7.4 Software package for signal-level analysis of Oxford Nanopore sequencing data. nanosim: nanosim/2.6.0-python-2.7.16, nanosim/2.6.0-python-3.7.4 NanoSim is a fast and scalable read simulator that captures the technology-specific features of ONT data, and allows for adjustments upon improvement of nanopore sequencing technology. nasm: nasm/2.14.02, nasm/2.15.05 NASM: General-purpose x86 assembler nbo: nbo/7.0 The Natural Bond Orbital (NBO) program is a discovery tool for chemical insights from complex wavefunctions. ncbi-vdb: ncbi-vdb/2.9.3 The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. nccl: nccl/2.4.8, nccl/2.8.3-cuda-11.1.1 The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective communication primitives that are performance optimized for NVIDIA GPUs. ncdf4: ncdf4/1.16.1-r-3.6.0, ncdf4/1.17-r-3.6.2, ncdf4/1.17 ncdf4: Interface to Unidata netCDF (version 4 or earlier) format data files ncl: ncl/6.6.2 NCL is an interpreted language designed specifically for scientific data analysis and visualization. nco: nco/4.8.1 manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5 ncurses: ncurses/6.0, ncurses/6.1-test, ncurses/6.1, ncurses/6.2 The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses. ncview: ncview/2.1.8 Ncview is a visual browser for netCDF format files. Typically you would use ncview to get a quick and easy, push-button look at your netCDF files. You can view simple movies of the data, view along various dimensions, take a look at the actual data values, change color maps, invert the data, etc. nektar: nektar/5.0.0 Nektar++ is a tensor product based finite element package designed to allow one to construct efficient classical low polynomial order h-type solvers (where h is the size of the finite element) as well as higher p-order piecewise polynomial order solvers. nemo3d: nemo3d/08-mar-2014 NEMO 3-D calculates eigenstates in (almost) arbitrarily shaped semiconductor structures in the typical column IV and III-V materials. Atoms are represented by the empirical tight binding model using s, sp3s*, or sp3d5s* models with or without spin. Strain is computed using the classical alence force field (VFF) with various Keating-like potentials. netcdf: netcdf/4.7.1 NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. netcdf-c++4: netcdf-c++4/4.3.0 NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. netcdf-fortran: netcdf-fortran/4.4.5, netcdf-fortran/4.5.2 NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. netcdf4-python: netcdf4-python/1.4.3-python-3.7.4, netcdf4-python/1.5.3-python-3.7.4 Python/numpy interface to netCDF. netlogo: netlogo/6.2.0-64 NetLogo is a multi-agent programmable modeling environment. It is used by tens of thousands of students, teachers and researchers worldwide. It also powers HubNet participatory simulations. It is authored by Uri Wilensky and developed at the CCL. nettle: nettle/3.5.1 Nettle is a cryptographic library that is designed to fit easily in more or less any context: In crypto toolkits for object-oriented languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, or even in kernel space. networkx: networkx/2.4-python-3.7.4 NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks. newmat: newmat/11 This C++ library is intended for scientists and engineers who need to manipulate a variety of types of matrices using standard matrix operations. Emphasis is on the kind of operations needed in statistical calculations such as least squares, linear equation solve and eigenvalues. ngs: ngs/2.9.3-java-11.0.2 NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. nibabel: nibabel/2.5.1-python-3.7.4 NiBabel provides read/write access to some common medical and neuroimaging file formats, including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, MINC1, MINC2, MGH and ECAT as well as Philips PAR/REC. We can read and write Freesurfer geometry, and read Freesurfer morphometry and annotation files. There is some very limited support for DICOM. NiBabel is the successor of PyNIfTI. nim: nim/1.0.0 Nim is a systems and applications programming language. ninja: ninja/1.9.0, ninja/1.10.1-python-3.8.6 Ninja is a small build system with a focus on speed. nlopt: nlopt/2.6.1 NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms. nltk: nltk/3.5-python-3.7.4 NLTK is a leading platform for building Python programs to work with human language data. nodejs: nodejs/12.16.1, nodejs/12.21.0 Node.js is a platform built on Chrome's JavaScript runtime for easily building fast, scalable network applications. Node.js uses an event-driven, non-blocking I/O model that makes it lightweight and efficient, perfect for data-intensive real-time applications that run across distributed devices. norgal: norgal/1.0-python-3.7.4 Norgal takes NGS sequencing reads as input and tries to assemble the mitochondrial genome using kmer frequencies. nspr: nspr/4.21 Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level and libc-like functions. nss: nss/3.45 Network Security Services (NSS) is a set of libraries designed to support cross-platform development of security-enabled client and server applications. nsync: nsync/1.24.0 nsync is a C library that exports various synchronization primitives, such as mutexes nullarbor: nullarbor/2.0.20191013 Pipeline to generate complete public health microbiology reports from sequenced isolates. numactl: numactl/2.0.12, numactl/2.0.13 The numactl program allows you to run your application program on specific cpu's and memory nodes. It does this by supplying a NUMA memory policy to the operating system before running your program. The libnuma library provides convenient ways for you to add NUMA memory policies into your own program. numba: numba/0.47.0-python-3.7.4 Numba is an Open Source NumPy-aware optimizing compiler for Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM compiler infrastructure to compile Python syntax to machine code. numpy: numpy/1.8.2-python-2.7.16, numpy/1.9.2-python-2.7.16, numpy/1.17.3-python-3.7.4, numpy/1.18.0-python-3.7.4 NumPy is the fundamental package for scientific computing with Python. It contains among other things: a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases. octave: octave/4.2.1 GNU Octave is a high-level interpreted language, primarily intended for numerical computations. octopus: octopus/9.2, octopus/10.1 Octopus is a scientific program aimed at the ab initio virtual experimentation on a hopefully ever-increasing range of system types. Electrons are described quantum-mechanically within density-functional theory (DFT), in its time-dependent form (TDDFT) when doing simulations in time. Nuclei are described classically as point particles. Electron-nucleus interaction is described within the pseudopotential approximation. openbabel: openbabel/3.1.1-python-3.7.4 Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. openblas: openblas/0.3.7, openblas/0.3.12 OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. opencv: opencv/3.4.7-python-2.7.16, opencv/3.4.7-python-3.7.4, opencv/4.0.1-python-3.7.4, opencv/4.3.0-python-3.7.4 OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products. openfast: openfast/2.3.0 OpenFAST is a wind turbine simulation tool which builds on FAST v8. openfoam: openfoam/v1906, openfoam/v1912, openfoam/6, openfoam/7, openfoam/8 OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. openjpeg: openjpeg/2.3.1 OpenJPEG is an open-source JPEG 2000 codec written in C language. It has been developed in order to promote the use of JPEG 2000, a still-image compression standard from the Joint Photographic Experts Group (JPEG). Since may 2015, it is officially recognized by ISO/IEC and ITU-T as a JPEG 2000 Reference Software. openmpi: openmpi/3.1.4, openmpi/3.1.6, openmpi/4.0.3-testing, openmpi/4.0.3-ucx-1.7.x-cuda-10.1.243, ... The Open MPI Project is an open source MPI-3 implementation. openpgm: openpgm/5.2.122 OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM) specification in RFC 3208 available at www.ietf.org. PGM is a reliable and scalable multicast protocol that enables receivers to detect loss, request retransmission of lost data, or notify an application of unrecoverable loss. PGM is a receiver-reliable protocol, which means the receiver is responsible for ensuring all data is received, absolving the sender of reception responsibility. openslide: openslide/3.4.1 OpenSlide is a C library that provides a simple interface to read whole-slide images (also known as virtual slides). openslide-python: openslide-python/1.1.1 OpenSlide Python is a Python interface to the OpenSlide library. opensmile: opensmile/3.0.0 openSMILE (open-source Speech and Music Interpretation by Large-space Extraction) is a complete and open-source toolkit for audio analysis, processing and classification especially targeted at speech and music applications, e.g. automatic speech recognition, speaker identification, emotion recognition, or beat tracking and chord detection. openssl: openssl/1.1.1f The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) protocols as well as a full-strength general purpose cryptography library. orca: orca/4.2.1 ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects. orthofinder: orthofinder/2.3.11 OrthoFinder: phylogenetic orthology inference for comparative genomics p11-kit: p11-kit/0.23.21 Provides a way to load and enumerate PKCS#11 modules. Provides a standard configuration setup for installing PKCS#11 modules in such a way that they're discoverable. Also solves problems with coordinating the use of PKCS#11 by different components or libraries living in the same process. p7zip: p7zip/16.02 p7zip is a quick port of 7z.exe and 7za.exe (command line version of 7zip) for Unix. 7-Zip is a file archiver with highest compression ratio. paml: paml/4.9i PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. pandoc: pandoc/2.5 If you need to convert files from one markup format into another, pandoc is your swiss-army knife pango: pango/1.42.4, pango/1.43.0, pango/1.44.7 Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x. papi: papi/5.7.0 PAPI provides the tool designer and application engineer with a consistent interface and methodology for use of the performance counter hardware found in most major microprocessors. PAPI enables software engineers to see, in near real time, the relation between software performance and processor events. In addition Component PAPI provides access to a collection of components that expose performance measurement opportunites across the hardware and software stack. parallel: parallel/20170422, parallel/20190922 parallel: Build and execute shell commands in parallel paraview: paraview/5.6.2-python-2.7.16-mpi, paraview/5.6.2-python-3.7.4-mpi ParaView is a scientific parallel visualizer. parmetis: parmetis/4.0.3 ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes. parsnp: parsnp/1.5.3 Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. patchelf: patchelf/0.10 PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables. pauvre: pauvre/0.2.2-python-3.7.4, pauvre/0.1923-python-3.7.4 Tools for plotting Oxford Nanopore and other long-read data pbbam: pbbam/1.6.0 The pbbam software package provides components to create, query, & edit PacBio BAM files and associated indices. These components include a core C++ library, bindings for additional languages, and command-line utilities. pbcopper: pbcopper/1.9.0 The pbcopper library provides a suite of data structures, algorithms, and utilities for PacBio C++ applications. pbsim: pbsim/20180330 PacBio sequencers produce two types of characteristic reads as below. pcap-core: pcap-core/5.3.0 This has been forked from the [ICGC-TCGA-PanCancer/PCAP-core][PCAP-core] repository as this codebase was created by cancerit and continues to be developed. This version strips out PCAWG related elements and incorporates more efficient code. pcre: pcre/8.43 The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. pcre2: pcre2/10.33 The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. perl: perl/5.30.0, perl/5.32.0 Larry Wall's Practical Extraction and Report Language pest: pest/15 Model-Independent Parameter Estimation and Uncertainty Analysis petsc: petsc/3.11.0-downloaded-deps, petsc/3.12.4 PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. pgi: pgi/18.10-gcc-8.3.0-2.32, pgi/19.7-gcc-8.3.0-2.32 C, C++ and Fortran compilers from The Portland Group - PGI phast: phast/1.5 PHAST is a freely available software package for comparative and evolutionary genomics. phastaf: phastaf/0.1.0 Identify phage regions in bacterial genomes for masking purposes phylip: phylip/3.697 PHYLIP is a free package of programs for inferring phylogenies. phyml: phyml/3.3.20200621 Phylogenetic estimation using (Maximum) Likelihood picard: picard/2.6.0-java-11.0.2 A set of tools (in Java) for working with next generation sequencing data in the BAM format. piggy: piggy/1.5 Piggy is a tool for analysing the intergenic component of bacterial genomes. pigz: pigz/2.4 pigz, which stands for parallel implementation of gzip, is a fully functional replacement for gzip that exploits multiple processors and multiple cores to the hilt when compressing data. pigz was written by Mark Adler, and uses the zlib and pthread libraries. pil: pil/1.1.7-python-2.7.16 The Python Imaging Library (PIL) adds image processing capabilities to your Python interpreter. This library supports many file formats, and provides powerful image processing and graphics capabilities. pillow: pillow/6.2.1, pillow/7.2.0-python-3.7.4, pillow/8.0.1-python-3.8.6 Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors. pillow-simd: pillow-simd/6.0.x.post0 Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors. pilon: pilon/1.23-java-11.0.2 Pilon is an automated genome assembly improvement and variant detection tool pirate: pirate/1.0.3 PIRATE provides a robust framework for analysing the pangenomes of bacteria, from largely clonal to panmictic species. pixman: pixman/0.38.0, pixman/0.38.4 Pixman is a low-level software library for pixel manipulation, providing features such as image compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server. pkg-config: pkg-config/0.29.2 pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the correct compiler options on the command line so an application can use gcc -o test test.c `pkg-config --libs --cflags glib-2.0` for instance, rather than hard-coding values on where to find glib (or other libraries). pkgconfig: pkgconfig/1.5.1-python-3.7.4 pkgconfig is a Python module to interface with the pkg-config command line tool platanus2: platanus2/2.2.2 Platanus-allee is a de novo haplotype assembler (phasing tool), which assembles each haplotype sequence in a diploid genome. plink: plink/1.9b_6.21-x86_64, plink/2.00-alpha2-x86_64_avx2 plink-1.9-x86_64: Whole-genome association analysis toolset plotly.py: plotly.py/4.4.1 An open-source, interactive graphing library for Python plumed: plumed/2.5.0-python-3.7.4, plumed/2.5.3-python-3.7.4, plumed/2.6.0-python-3.7.4, plumed/2.6.2-python-3.7.4 PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. ply: ply/3.11-python-3.7.4 PLY is yet another implementation of lex and yacc for Python. pmix: pmix/3.1.5 Process Management for Exascale Environments PMI Exascale (PMIx) represents an attempt to provide an extended version of the PMI standard specifically designed to support clusters up to and including exascale sizes. The overall objective of the project is not to branch the existing pseudo-standard definitions - in fact, PMIx fully supports both of the existing PMI-1 and PMI-2 APIs - but rather to (a) augment and extend those APIs to eliminate some current restrictions that impact scalability, and (b) provide a reference implementation of the PMI-server that demonstrates the desired level of scalability. pnetcdf: pnetcdf/1.10.0 Parallel netCDF: A Parallel I/O Library for NetCDF File Access poppler: poppler/0.87.0 Poppler is a PDF rendering library based on the xpdf-3.0 code base. poppunk: poppunk/1.1.3-python-3.7.4 PopPUNK (POPulation Partitioning Using Nucleotide Kmers) porechop: porechop/0.2.4-python-3.7.4 Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads. Porechop performs thorough alignments to effectively find adapters, even at low sequence identity pplacer: pplacer/1.1.alpha19 Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment. Pplacer is designed to be fast, to give useful information about uncertainty, and to offer advanced visualization and downstream analysis. prank: prank/170427 PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences. PRANK is based on a novel algorithm that treats insertions correctly and avoids over-estimation of the number of deletion events. primus: primus/1.9.0 PRIMUS: Pedigree Reconstruction and Identification of a Maximum Unrelated Set. prodigal: prodigal/2.6.3 Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee. proj: proj/4.9.3, proj/5.2.0, proj/6.2.1 Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates prokka: prokka/1.14.5 Prokka is a software tool for the rapid annotation of prokaryotic genomes. protobuf: protobuf/3.7.1, protobuf/3.10.0, protobuf/3.14.0 Google Protocol Buffers protobuf-python: protobuf-python/3.10.0-python-3.7.4, protobuf-python/3.14.0-python-3.8.6 Python Protocol Buffers runtime library. pspm: pspm/4.3.0 PsPM stands for PsychoPhysiological Modelling. It is a powerful matlab toolbox for model-based analysis of psychophysiological signals. pugixml: pugixml/1.10 pugixml is a C++ XML processing library, which consists of a DOM-like interface with rich traversal/modification capabilities, an extremely fast XML parser which constructs the DOM tree from an XML file/buffer, and an XPath 1.0 implementation for complex data-driven tree queries. pybind11: pybind11/2.4.3-python-3.7.4, pybind11/2.6.0-python-3.8.6 pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, mainly to create Python bindings of existing C++ code. pycharm: pycharm/2019.3.1 PyCharm Community Edition: Python IDE for Professional Developers pyopengl: pyopengl/3.1.3b2-python-2.7.16 PyOpenGL is the most common cross platform Python binding to OpenGL and related APIs. pyqt5: pyqt5/5.12.1-python-2.7.16, pyqt5/5.12.1-python-3.7.4 PyQt5 is a set of Python bindings for v5 of the Qt application framework from The Qt Company. This bundle includes PyQtWebEngine, a set of Python bindings for The Qt Company’s Qt WebEngine framework. pysam: pysam/0.15.3 Pysam is a python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix. pyscaf: pyscaf/0.12a4-python-2.7.16 pyScaf orders contigs from genome assemblies utilising several types of information pytest: pytest/6.0.1-python-3.7.4 pytest: simple powerful testing with Python pythia: pythia/8.2 PYTHIA 8 is the successor to PYTHIA 6, rewritten from scratch in C++. At the release of the first public version, 8.100, it was untried and also still missed a few relevant features. This has changed over the years since then, and the release of 8.200 marks the end of a transition period. PYTHIA 8.2 has a significantly extended physics scope, notably for LHC physics, relative to what PYTHIA 6.4 could offer. There are only a few areas left where 6.4 still has a role to fill. python: python/2.7.16, python/3.7.4, python/3.8.2, python/3.8.6 Python is a programming language that lets you work more quickly and integrate your systems more effectively. python-bioformats: python-bioformats/4.0.0-python-3.7.4 Python-bioformats is a Python wrapper for Bio-Formats, a standalone Java library for reading and writing life sciences image file formats. Bio-Formats is capable of parsing both pixels and metadata for a large number of formats, as well as writing to several formats. Python-bioformats uses the python-javabridge to start a Java virtual machine from Python and interact with it. Python-bioformats was developed for and is used by the cell image analysis software CellProfiler (cellprofiler.org). pytorch: pytorch/1.4.0-python-3.7.4, pytorch/1.5.1-python-3.7.4, pytorch/1.7.1-python-3.8.6 Tensors and Dynamic neural networks in Python with strong GPU acceleration. PyTorch is a deep learning framework that puts Python first. pytorch-geometric: pytorch-geometric/1.6.1-python-3.7.4-pytorch-1.6.0 PyTorch Geometric (PyG) is a geometric deep learning extension library for PyTorch. pyyaml: pyyaml/5.1.2, pyyaml/5.3.1-python-3.8.6 PyYAML is a YAML parser and emitter for the Python programming language. qctool: qctool/2.0.8 qctool v2 tool for quality control and analysis of gwas datasets. . qhull: qhull/2015.2, qhull/2019.1 Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull. qiime2: qiime2/2020.2, qiime2/2021.2 QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data. qrupdate: qrupdate/1.1.2 qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions. qt: qt/4.8.6 Qt is a comprehensive cross-platform C++ application framework. qt5: qt5/5.13.1 Qt is a comprehensive cross-platform C++ application framework. qualimap: qualimap/2.2.1-r-3.6.0 Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts. quantumespresso: quantumespresso/6.6 Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft). quast: quast/5.0.2-python-3.7.4 QUAST evaluates genome assemblies by computing various metrics. It works both with and without reference genomes. The tool accepts multiple assemblies, thus is suitable for comparison. qwt: qwt/6.1.4 The Qwt library contains GUI Components and utility classes which are primarily useful for programs with a technical background. r: r/3.6.0, r/3.6.2, r/4.0.0 R is a free software environment for statistical computing and graphics. r-bundle-bioconductor: r-bundle-bioconductor/3.9-r-3.6.0, r-bundle-bioconductor/3.10-r-3.6.2 Bioconductor provides tools for the analysis and coprehension of high-throughput genomic data. racon: racon/1.4.7 Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. randfold: randfold/2.0.1 Minimum free energy of folding randomization test software rapidjson: rapidjson/1.1.0 A fast JSON parser/generator for C++ with both SAX/DOM style API raspa2: raspa2/2.0.38 Classical molecular simulation code raxml: raxml/8.2.12-hybrid-avx, raxml/8.2.12-pthreads-sse3 RAxML search algorithm for maximum likelihood based inference of phylogenetic trees. rcorrector: rcorrector/1.0.2 Rcorrector(RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data. rdkit: rdkit/2019.09.3-python-3.7.4 RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python. re2c: re2c/1.2.1 re2c is a free and open-source lexer generator for C and C++. Its main goal is generating fast lexers: at least as fast as their reasonably optimized hand-coded counterparts. Instead of using traditional table-driven approach, re2c encodes the generated finite state automata directly in the form of conditional jumps and comparisons. redundans: redundans/0.14a Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes. reforge: reforge/20200207 REforge (Regulatory Element forward genomics) is a method to associate transciption factor binding site divergence in regulatory elements with phenotypic differences between species. regtools: regtools/0.5.2 Tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context. relion: relion/3.0.4, relion/3.1.0-test, relion/3.1.0 RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM). Note that you must use --gpu flags to take advantage of this version's acceleration features. renderproto: renderproto/0.11 Xrender protocol and ancillary headers requests: requests/2.13.0-python-2.7.16 Python http for humans rgdal: rgdal/1.4-4-r-3.6.0, rgdal/1.4-8-r-3.6.2, rgdal/1.5-16-r-4.0.0 Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.11.4 and <= 2.5.0) and access to projection/transformation operations from the 'PROJ.4' library. riblast: riblast/1.2.0 RIblast is ultrafast RNA-RNA interaction prediction software based on seed-and-extension algorithm for comprehensive lncRNA interactome analysis. rmats: rmats/4.1.0 MATS is a computational tool to detect differential alternative splicing events from RNA-Seq data. rnahybrid: rnahybrid/2.1.2 RNAhybrid is a tool for finding the minimum free energy hybridization of a long and a short RNA. The hybridization is performed in a kind of domain mode, ie. the short sequence is hybridized to the best fitting part of the long one. The tool is primarily meant as a means for microRNA target prediction. rnammer: rnammer/1.2 Prediction of ribosomal RNA sub units rnaquast: rnaquast/2.2.0-python-3.7.4 rnaQUAST is a tool for evaluating RNA-Seq assemblies using reference genome and gene database. In addition, rnaQUAST is also capable of estimating gene database coverage by raw reads and de novo quality assessment using third-party software. roary: roary/3.12.0-perl-5.30.0, roary/3.12.0 Rapid large-scale prokaryote pan genome analysis root: root/6.14.06-python-2.7.16, root/6.19.01-python-2.7.16, root/6.22.02-python-3.7.4, root/6.22.02-python-3.8.2 The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data in a very efficient way. rpy2: rpy2/3.2.6-python-3.7.4 rpy2 is an interface to R running embedded in a Python process. rsem: rsem/1.3.2 RNA-Seq by Expectation-Maximization ruby: ruby/2.6.3 Ruby is a dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write. rust: rust/1.37.0, rust/1.48.0 Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety. salmon: salmon/0.8.2, salmon/1.0.0 Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. samclip: samclip/0.2-perl-5.30.0 Filter SAM file for soft and hard clipped alignments samstat: samstat/1.5.1 Displaying sequence statistics for next generation sequencing samtools: samtools/1.9, samtools/1.12 SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. savvy: savvy/1.3.0 Interface to various variant calling formats. scalapack: scalapack/2.0.2, scalapack/2.1.0 The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers. scientificpython: scientificpython/2.9.4-python-2.7.16 ScientificPython is a collection of Python modules for scientific computing. It contains support for geometry, mathematical functions, statistics, physical units, IO, visualization, and parallelization. scikit-bio: scikit-bio/0.5.6-python-3.7.4 scikit-bio is an open-source, BSD-licensed, Python package providing data structures, algorithms, and educational resources for bioinformatics.. scikit-build: scikit-build/0.10.0-python-3.7.4 Scikit-Build, or skbuild, is an improved build system generator for CPython C/C++/Fortran/Cython extensions. scikit-image: scikit-image/0.16.2-python-3.7.4 scikit-image is a collection of algorithms for image processing. scikit-learn: scikit-learn/0.20.4-python-2.7.16, scikit-learn/0.21.3-python-3.7.4, scikit-learn/0.23.1-python-3.7.4 Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. It strives to be simple and efficient, accessible to everybody, and reusable in various contexts. scikit-surprise: scikit-surprise/1.1.1-python-3.7.4 Surprise is a Python scikit for building and analyzing recommender systems that deal with explicit rating data. scipy-bundle: scipy-bundle/2019.03, scipy-bundle/2019.10-python-2.7.16, scipy-bundle/2019.10-python-3.7.4, scipy-bundle/2019.10, ... Bundle of Python packages for scientific software scons: scons/3.1.1 SCons is a software construction tool. scotch: scotch/6.0.9 Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning. screen_assembly: screen_assembly/1.2.7-python-3.7.4 Pipeline that screens for presence of genes of interest (GOI) in bacterial assemblies. scythe: scythe/0.994 Scythe uses a Naive Bayesian approach to classify contaminant substrings in sequence reads. It considers quality information, which can make it robust in picking out 3'-end adapters, which often include poor quality bases. sdl2: sdl2/2.0.9 SDL: Simple DirectMedia Layer, a cross-platform multimedia library sdsl: sdsl/2.1.1-20191211 The Succinct Data Structure Library (SDSL) is a powerful and flexible C++11 library implementing succinct data structures. seaborn: seaborn/0.9.0-python-3.7.4, seaborn/0.10.0-python-3.7.4, seaborn/0.10.1-python-3.7.4, seaborn/0.11.1-python-3.7.4 Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics. semtex: semtex/9.3 Semtex is a 'classical' quadrilateral spectral element DNS code that uses the standard nodal GLL basis functions and (optionally) Fourier expansions in a homogeneous direction to provide three-dimensional solutions. If your problem has a natural periodic coordinate direction in 3D (a cylindrical coordinate system is perhaps the most obvious example), semtex could be a good choice. For 3D problems of this kind, the code can run in parallel using MPI to distribute jobs over a number of processes; semtex is equally at home on Unix machines from laptop to supercomputer. sentencepiece: sentencepiece/0.1.94-python-3.7.4 Unsupervised text tokenizer for Neural Network-based text generation. sepp: sepp/4.3.10-python-3.7.4 SATe-enabled Phylogenetic Placement - addresses the problem of phylogenetic placement of short reads into reference alignments and trees. seqtk: seqtk/1.3 Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip. serf: serf/1.3.9 The serf library is a high performance C-based HTTP client library built upon the Apache Portable Runtime (APR) library sextractor: sextractor/2.25.0 SExtractor is a program that builds a catalogue of objects from an astronomical image. Although it is particularly oriented towards reduction of large scale galaxy-survey data, it can perform reasonably well on moderately crowded star fields. sharedmem: sharedmem/0.3.5-python-3.7.4 A different flavor of multiprocessing in Python shovill: shovill/1.0.4-python-2.7.16 Faster SPAdes assembly of Illumina reads showq: showq/0.12, showq/0.15 shrinkwrap: shrinkwrap/1.0.0-beta A std::streambuf wrapper for compression formats. sickle: sickle/1.33 Windowed Adaptive Trimming for fastq files using quality siesta: siesta/4.0.2 SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. signalp: signalp/5.0b Signal peptide and cleavage sites in gram+, gram- and eukaryotic amino acid sequences singularity: singularity/2.5.2, singularity/3.5.3, singularity/3.6.3, singularity/3.7.3 Singularity is a portable application stack packaging and runtime utility. skesa: skesa/2.3.0 SKESA is a de-novo sequence read assembler for cultured single isolate genomes based on DeBruijn graphs. slepc: slepc/3.12.2 SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems. sleuth: sleuth/0.30.0-r-3.6.0 Investigate RNA-Seq transcript abundance from kallisto and perform differential expression analysis. slim: slim/3.5, slim/3.6 SLiM is an evolutionary simulation framework that combines a powerful engine for population genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios. slurm: slurm/latest snakemake: snakemake/5.18.1 The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. snap: snap/1.0beta.24 Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data snappy: snappy/1.1.7 Snappy is a compression/decompression library. It does not aim for maximum compression, or compatibility with any other compression library; instead, it aims for very high speeds and reasonable compression. snippy: snippy/4.4.1-perl-5.30.0, snippy/4.6.0-perl-5.30.0 Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels). Rapid haploid variant calling and core genome alignment. snp-sites: snp-sites/2.4.1 Rapidly decreasing genome sequencing costs have led to a proportionate increase in the number of samples used in prokaryotic population studies. snpeff: snpeff/4.1d-java-11.0.2, snpeff/5.0-java-11.0.2 SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes). snphylo: snphylo/20160204 With this pipeline, user can construct a phylogenetic tree from a file containing huge SNP data. soapdenovo2: soapdenovo2/r241 SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for human-sized genomes. The program is specially designed to assemble Illumina short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. SOAPdenovo2 is the successor of SOAPdenovo. somalier: somalier/0.2.10 Extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF spades: spades/3.13.0, spades/3.14.0-python-3.7.4, spades/3.14.1-python-3.7.4 Genome assembler for single-cell and isolates data sets sparsehash: sparsehash/2.0.3 An extremely memory-efficient hash_map implementation. 2 bits/entry overhead! The SparseHash library contains several hash-map implementations, including implementations that optimize for space or speed. spartan: spartan/2016-03-parallel, spartan/2016-03 sqlite: sqlite/3.29.0, sqlite/3.32.3, sqlite/3.33.0 SQLite: SQL Database Engine in a C Library sra-toolkit: sra-toolkit/2.9.6-1-centos_linux64, sra-toolkit/2.10.5-centos_linux64 The SRA Toolkit, and the source-code SRA System Development Kit (SDK), will allow you to programmatically access data housed within SRA and convert it from the SRA format sspace_basic: sspace_basic/2.1.1-perl-5.30.0 SSPACE Basic, SSAKE-based Scaffolding of Pre-Assembled Contigs after Extension stacks: stacks/2.53 Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography. star: star/2.7.3a STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays. stata: stata/15, stata/16-legacy Stata is a complete, integrated statistical software package that provides everything you need for data analysis, data management, and graphics. statsmodels: statsmodels/0.11.0-python-3.7.4 Statsmodels is a Python module that allows users to explore data, estimate statistical models, and perform statistical tests. strelka: strelka/2.9.10-python-2.7.16 Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation in small cohorts and somatic variation in tumor/normal sample pairs. stringtie: stringtie/2.1.0 StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts structure: structure/2.3.4 The program structure is a free software package for using multi-locus genotype data to investigate population structure. stubb: stubb/2.1-reforge For finding cis-regulatory modules - NB: this version patched for use with REforge. subread: subread/2.0.0 High performance read alignment, quantification and mutation discovery subversion: subversion/1.13.0, subversion/1.14.0 Subversion is an open source version control system. suitesparse: suitesparse/5.4.0-metis-5.1.0, suitesparse/5.6.0-metis-5.1.0 SuiteSparse is a collection of libraries manipulate sparse matrices. sundials: sundials/5.1.0 SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers supernova: supernova/2.1.1 Supernova is a software package for de novo assembly from Chromium Linked-Reads that are made from a single whole-genome library from an individual DNA source swig: swig/3.0.12-python-2.7.16, swig/3.0.12-python-3.7.4, swig/4.0.1 SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages. szip: szip/2.1.1 Szip compression software, providing lossless compression of scientific data t-coffee: t-coffee/13.41.0, t-coffee/13.41.139, t-coffee/13.43.2.1, t-coffee/13.44.4.6104691 tabix: tabix/0.2.6 Generic indexer for TAB-delimited genome position files tbb: tbb/2019_u9, tbb/2020.3 Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that take full advantage of multicore performance, that are portable, composable and have future-proof scalability. tbl2asn: tbl2asn/3.10.0 Tbl2asn is a command-line program that automates the creation of sequence records for submission to GenBank tcl: tcl/8.6.8, tcl/8.6.9, tcl/8.6.10 Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more. tcsh: tcsh/6.22.02 Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). It is a command language interpreter usable both as an interactive login shell and a shell script command processor. It includes a command-line editor, programmable word completion, spelling correction, a history mechanism, job control and a C-like syntax. tensorflow: tensorflow/1.15.0-python-3.7.4, tensorflow/1.15.2-python-3.7.4, tensorflow/2.1.0-python-3.7.4, ... An open-source software library for Machine Intelligence tetgen: tetgen/1.5.0 A Quality Tetrahedral Mesh Generator and a 3D Delaunay Triangulator texinfo: texinfo/6.6, texinfo/6.7 Texinfo is the official documentation format of the GNU project. texlive: texlive/2019, texlive/20200406 TeX Live is an easy way to get up and running with the TeX document production system. It provides a comprehensive TeX system with binaries for most flavors of Unix, including GNU/Linux, and also Windows. It includes all the major TeX-related programs, macro packages, and fonts that are free software, including support for many languages around the world. theano: theano/1.0.4 Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently. tinyxml: tinyxml/2.6.2 TinyXML is a simple, small, minimal, C++ XML parser that can be easily integrating into other programs. It reads XML and creates C++ objects representing the XML document. The objects can be manipulated, changed, and saved again as XML. tk: tk/8.6.9 Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building a graphical user interface (GUI) in many different programming languages. tkinter: tkinter/2.7.16, tkinter/3.7.4 Tkinter module, built with the Python buildsystem tmhmm: tmhmm/2.0c-perl-5.30.0 Prediction of transmembrane helices in proteins tmux: tmux/3.0 tmux is a terminal multiplexer. It lets you switch easily between several programs in one terminal, detach them (they keep running in the background) and reattach them to a different terminal. torch: torch/20200428 Torch is a scientific computing framework with wide support for machine learning algorithms that puts GPUs first. It is easy to use and efficient, thanks to an easy and fast scripting language, LuaJIT, and an underlying C/CUDA implementation. torchvision: torchvision/0.5.0-python-3.7.4 Datasets, Transforms and Models specific to Computer Vision tpmcalculator: tpmcalculator/0.0.3 TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files tqdm: tqdm/4.41.1-python-3.7.4, tqdm/4.41.1 A fast, extensible progress bar for Python and CLI tract_querier: tract_querier/20200407-python-3.7.4 The White Matter Query Language (WMQL) is a technique to formally describe white matter tracts and to automatically extract them from diffusion MRI volumes. transdecoder: transdecoder/5.5.0-perl-5.30.0 TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. transrate: transrate/1.0.3 Transrate is software for de-novo transcriptome assembly quality analysis. It examines your assembly in detail and compares it to experimental evidence such as the sequencing reads, reporting quality scores for contigs and assemblies. This allows you to choose between assemblers and parameters, filter out the bad contigs from an assembly, and help decide when to stop trying to improve the assembly. trf: trf/4.09-linux64 Tandem repeats finder: a program to analyze DNA sequences. Legacy version. triangle: triangle/1.6 Triangle generates exact Delaunay triangulations, constrained Delaunay triangulations, conforming Delaunay triangulations, Voronoi diagrams, and high-quality triangular meshes. The latter can be generated with no small or large angles, and are thus suitable for finite element analysis. trim_galore: trim_galore/0.6.5-java-11.0.2-python-3.7.4 Trim Galore is a wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data. trimal: trimal/1.4.1 A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0 trimmomatic: trimmomatic/0.39-java-11.0.2 Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line. trinity: trinity/2.10.0, trinity/2.11.0 Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads. trinotate: trinotate/3.2.1 Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. trycycler: trycycler/0.3.3-python-3.7.4 Trycycler is a tool for generating consensus long-read assemblies for bacterial genomes. I.e. if you have multiple long-read assemblies for the same isolate, Trycycler can combine them into a single assembly that is better than any of your inputs. turbovnc: turbovnc/2.2.3 TurboVNC is a derivative of VNC (Virtual Network Computing) that is tuned to provide peak performance for 3D and video workloads. typing-extensions: typing-extensions/3.7.4.3-python-3.8.6 Typing Extensions – Backported and Experimental Type Hints for Python ucsc: ucsc/21072020 This directory contains ucsc applications for stand-alone use. ucx: ucx/1.7.x-cuda-10.1.243, ucx/1.8.1-nocuda Unified Communication X An open-source production grade communication framework for data centric and high-performance applications udunits: udunits/2.2.26 UDUNITS supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of units, and conversion of values between compatible scales of measurement. ufl: ufl/2018.1.0-python-3.7.4 The Unified Form Language (UFL) is a domain specific language for declaration of finite element discretizations of variational forms. More precisely, it defines a flexible interface for choosing finite element spaces and defining expressions for weak forms in a notation close to mathematical notation. unicycler: unicycler/0.4.8-python-3.7.4 Unicycler is an assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets where it functions as a SPAdes-optimiser. It can also assembly long-read-only sets (PacBio or Nanopore) where it runs a miniasm+Racon pipeline. unimelb-mf-clients: unimelb-mf-clients/current unimelb-mf-clients is a collection of command-line tools to transfer data to/from Mediaflux, the data management platform operated by Research Computing Services unittest-cpp: unittest-cpp/2.0.0 A lightweight unit testing framework for C++. unrar: unrar/5.7.3 RAR is a powerful archive manager. unzip: unzip/6.0 UnZip is an extraction utility for archives compressed in .zip format (also called "zipfiles"). Although highly compatible both with PKWARE's PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP's own Zip program, our primary objectives have been portability and non-MSDOS functionality. upcxx-utils: upcxx-utils/0.3.4 Utilities to assist in development of UPC++ oriented applications usearch: usearch/11.0.667-i86linux32 USEARCH is a unique sequence analysis tool which offers search and clustering algorithms that are often orders of magnitude faster than BLAST. utf8proc: utf8proc/2.3.0 utf8proc is a small, clean C library that provides Unicode normalization, case-folding, and other operations for data in the UTF-8 encoding. util-linux: util-linux/2.34, util-linux/2.36 Set of Linux utilities v8: v8/3.4.0-r-3.6.2 R interface to Google's open source JavaScript engine valgrind: valgrind/3.13.0, valgrind/3.14.0 Valgrind: Debugging and profiling tools varscan: varscan/2.4.4-java-11.0.2 Variant calling and somatic mutation/CNV detection for next-generation sequencing data vcftools: vcftools/0.1.16 The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files. velvet: velvet/1.2.10-mt-kmer_191 Sequence assembler for very short reads velvetoptimiser: velvetoptimiser/2.2.5 VelvetOptimiser is a multi-threaded Perl script for automatically optimising the three primary parameter options (K, -exp_cov, -cov_cutoff) for the Velvet de novo sequence assembler. vep: vep/96.0-perl-5.30.0, vep/100.4-perl-5.30.0, vep/101.0-perl-5.30.0, vep/103.1-perl-5.30.0 Variant Effect Predictor (VEP) determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. Includes EnsEMBL-XS, which provides pre-compiled replacements for frequently used routines in VEP. viennarna: viennarna/2.4.10-python-3.7.4, viennarna/2.4.17-python-3.7.4 The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures. vmd: vmd/1.9.3-python-2.7.16 VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. voro++: voro++/0.4.6 Voro++ is a software library for carrying out three-dimensional computations of the Voronoi tessellation. A distinguishing feature of the Voro++ library is that it carries out cell-based calculations, computing the Voronoi cell for each particle individually. It is particularly well-suited for applications that rely on cell-based statistics, where features of Voronoi cells (eg. volume, centroid, number of faces) can be used to analyze a system of particles. vsearch: vsearch/2.9.1, vsearch/2.14.2 VSEARCH supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, rereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering, conversion and merging of paired-end reads. vt: vt/0.57721 A tool set for short variant discovery in genetic sequence data. vtk: vtk/8.2.0-python-2.7.16, vtk/8.2.0-python-3.7.4 The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation. w2rap-contigger: w2rap-contigger/0.1 An Illumina PE genome contig assembler, can handle large (17Gbp) complex (hexaploid) genomes. wannier90: wannier90/3.0.0 A tool for obtaining maximally-localised Wannier functions wcwidth: wcwidth/0.1.8-python-2.7.16 wcwidth is a low-level Python library to simplify Terminal emulation. web_proxy: web_proxy/latest, web_proxy/1.0 webkitgtk+: webkitgtk+/2.24.1 WebKitGTK+ is a full-featured port of the WebKit rendering engine, suitable for projects requiring any kind of web integration, from hybrid HTML/CSS applications to full-fledged web browsers. It offers WebKit.s full functionality and is useful in a wide range of systems from desktop computers to embedded systems like phones, tablets, and televisions. wget: wget/1.20.1 GNU Wget is a free software package for retrieving files using HTTP, HTTPS and FTP, the most widely-used Internet protocols. It is a non-interactive commandline tool, so it may easily be called from scripts, cron jobs, terminals without X-Windows support, etc. wgsim: wgsim/20111018 Wgsim is a small tool for simulating sequence reads from a reference genome. wine: wine/4.0.4 Wine: Free implementation of Windows on Unix wxpython: wxpython/4.0.7-python-3.7.4 wxPython is a GUI toolkit for the Python programming language. It allows Python programmers to create programs with a robust, highly functional graphical user interface, simply and easily. It is implemented as a Python extension module (native code) that wraps the popular wxWidgets cross platform GUI library, which is written in C++. wxwidgets: wxwidgets/3.0.3, wxwidgets/3.1.3 wxWidgets is a C++ library that lets developers create applications for Windows, Mac OS X, Linux and other platforms with a single code base. It has popular language bindings for Python, Perl, Ruby and many other languages, and unlike other cross-platform toolkits, wxWidgets gives applications a truly native look and feel because it uses the platform's native API rather than emulating the GUI. x11: x11/20190717, x11/20201008 The X Window System (X11) is a windowing system for bitmap displays x264: x264/20190925, x264/20201026 x264 is a free software library and application for encoding video streams into the H.264/MPEG-4 AVC compression format, and is released under the terms of the GNU GPL. x265: x265/3.2, x265/3.3 x265 is a free software library and application for encoding video streams into the H.265 AVC compression format, and is released under the terms of the GNU GPL. xcb-proto: xcb-proto/1.11 The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility. xdg-dbus-proxy: xdg-dbus-proxy/0.1.2 xdg-dbus-proxy is a filtering proxy for D-Bus connections. It was originally part of the flatpak project, but it has been broken out as a standalone module to facilitate using it in other contexts. xerces-c++: xerces-c++/3.2.2 Xerces-C++ is a validating XML parser written in a portable subset of C++. Xerces-C++ makes it easy to give your application the ability to read and write XML data. A shared library is provided for parsing, generating, manipulating, and validating XML documents using the DOM, SAX, and SAX2 APIs. xextproto: xextproto/7.3.0 XExtProto protocol headers. xml-parser: xml-parser/2.44_01-perl-5.30.0 This is a Perl extension interface to James Clark's XML parser, expat. xorg-macros: xorg-macros/1.19.2 X.org macros utilities. xpore: xpore/0.5.6-python-3.7.4, xpore/1.0-python-3.7.4 Python package for detection of differential RNA modifications from direct RNA sequencing. xprop: xprop/1.2.4 The xprop utility is for displaying window and font properties in an X server. One window or font is selected using the command line arguments or possibly in the case of a window, by clicking on the desired window. A list of properties is then given, possibly with formatting information. xproto: xproto/7.0.31 X protocol and ancillary headers xsd: xsd/4.0.0 CodeSynthesis XSD is an open-source, cross-platform W3C XML Schema to C++ data binding compiler. xsv: xsv/0.13.0 A fast CSV command line toolkit written in Rust. xtrans: xtrans/1.3.5 xtrans includes a number of routines to make X implementations transport-independent; at time of writing, it includes support for UNIX sockets, IPv4, IPv6, and DECnet. xvfb: xvfb/1.20.8 Xvfb is an X server that can run on machines with no display hardware and no physical input devices. It emulates a dumb framebuffer using virtual memory. xz: xz/5.2.4, xz/5.2.5 xz: XZ utilities yaff: yaff/1.6.0-python-3.7.4 Yaff stands for 'Yet another force field'. It is a pythonic force-field code. yaml-cpp: yaml-cpp/0.6.3 yaml-cpp is a YAML parser and emitter in C++ matching the YAML 1.2 spec. yasm: yasm/1.3.0 Yasm: Complete rewrite of the NASM assembler with BSD license yaxt: yaxt/0.6.2 Yet Another eXchange Tool zeromq: zeromq/4.3.2 ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. It gives you sockets that carry atomic messages across various transports like in-process, inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous message-processing tasks. It has a score of language APIs and runs on most operating systems. zip: zip/3.0 Zip is a compression and file packaging/archive utility. Although highly compatible both with PKWARE's PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP's own UnZip, our primary objectives have been portability and other-than-MSDOS functionality zlib: zlib/1.2.8, zlib/1.2.11-testing, zlib/1.2.11 zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system. zsh: zsh/5.8 Zsh is a shell designed for interactive use, although it is also a powerful scripting language. zstd: zstd/1.4.0, zstd/1.4.4 Zstandard is a real-time compression algorithm, providing high compression ratios. It offers a very wide range of compression/speed trade-off, while being backed by a very fast decoder. It also offers a special mode for small data, called dictionary compression, and can create dictionaries from any sample set. ---------------------------------------------------------------------------------------------------------------------------------------- To learn more about a package execute: $ module spider Foo where "Foo" is the name of a module. To find detailed information about a particular package you must specify the version if there is more than one version: $ module spider Foo/11.1 ----------------------------------------------------------------------------------------------------------------------------------------