---------------------------------------------------------------------------- The following is a list of the modules and extensions currently available: ---------------------------------------------------------------------------- EasyBuild: EasyBuild/latest, EasyBuild/3.9.3, 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. abaqus: abaqus/2017-hotfix-1721, abaqus/2020-hotfix-2243, abaqus/2020, ... 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 abseil: abseil/20210324.2 The repository contains the Abseil C++ library code. Abseil is an open-source collection of C++ code (compliant to C++11) designed to augment the C++ standard library. 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/22.0.06-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, almosthere/2.0.2 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. alphafold: alphafold/2.2.0 AlphaFold is an artificial intelligence (AI) program developed by DeepMind, a subsidiary of Alphabet, which performs predictions of protein structure. It is implemented as an Apptainer container on Spartan ambertools: ambertools/21 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. ampl-mp: ampl-mp/3.1.0 An open-source library for mathematical programming. 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, ... 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. angsd: angsd/0.921, angsd/0.935, angsd/0.938 Program for analysing NGS data. ansys_cfd: ansys_cfd/20.1, ansys_cfd/21.1 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, ... 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/2.3.5, ants/2.4.1 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 apptainer: apptainer/1.0.3 Apptainer is a portable application stack packaging and runtime utility. It replaces Singularity apr: apr/1.7.0 Apache Portable Runtime (APR) libraries. apr-util: apr-util/1.6.1 Apache Portable Runtime (APR) util libraries. arb: arb/7.0 The ARB software is a graphically oriented package comprising various tools for sequence database handling and data analysis. A central database of processed (aligned) sequences and any type of additional data linked to the respective sequence entries is structured according to phylogeny or other user defined criteria. archspec: archspec/0.1.0-python-2.7.16, 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/10.5.0 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-ng/3.8.0 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. aspera-connect: aspera-connect/3.11.2 Connect is an install-on-demand Web browser plug-in that facilitates high-speed uploads and downloads with an Aspera transfer server. assembly-stats: assembly-stats/1.0.1 Get assembly statistics from FASTA and FASTQ files. at-spi2-atk: at-spi2-atk/2.34.1, at-spi2-atk/2.38.0 AT-SPI 2 toolkit bridge at-spi2-core: at-spi2-core/2.34.0, at-spi2-core/2.38.0 Assistive Technology Service Provider Interface. atk: atk/2.34.1, atk/2.36.0 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. atlaas: atlaas/2022.03.08 ATLaAS stands for Analysis Tools for Low-coverage and Ancient Samples. These tools cover all programs necessary to obtain variant calls, estimates of heterozygosity and more from a BAM file. There are sequence data processing tools, diagnostic tools, and variant discovery tools, similar to GATK by the Broad Institute. 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/3.4.0 AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences autoconf: autoconf/2.69, autoconf/2.71 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. autoconf-archive: autoconf-archive/2021.02.19 The GNU Autoconf Archive is a collection of more than 500 macros for GNU Autoconf that have been contributed as free software by friendly supporters of the cause from all over the Internet. Every single one of those macros can be re-used without imposing any restrictions whatsoever on the licensing of the generated configure script. In particular, it is possible to use all those macros in configure scripts that are meant for non-free software. This policy is unusual for a Free Software Foundation project. The FSF firmly believes that software ought to be free, and software licenses like the GPL are specifically designed to ensure that derivative work based on free software must be free as well. In case of Autoconf, however, an exception has been made, because Autoconf is at such a pivotal position in the software development tool chain that the benefits from having this tool available as widely as possible outweigh the disadvantage that some authors may choose to use it, too, for proprietary software. 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 babl: babl/0.1.86 babl is pixel encoding and color space conversion engine in C 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/2.5.2 BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files. bamutil: bamutil/1.0.15 BamUtil is a repository that contains several programs that perform operations on SAM/BAM files. All of these programs are built into a single executable, bam. 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 basespacecli: basespacecli/1.5.3 BaseSpace is a powerful website where biologists and informaticians can easily store, analyze, and share genetic data. BaseSpace is a commerical product from Illumina. bazel: bazel/0.26.1, bazel/0.29.1, bazel/1.1.0, bazel/3.4.1, bazel/3.7.2 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/1.11, bcftools/1.12, bcftools/1.14, ... 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 bcl2fastq2: bcl2fastq2/2.20.0 bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis. beagle-lib: beagle-lib/3.0.2, beagle-lib/3.1.2 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/1.8.4, 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. bedops: bedops/2.4.35, bedops/2.4.40 BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for distributing whole-genome analyses across a computational cluster. bedtools: bedtools/2.27.1, bedtools/2.29.2, bedtools/2.30.0 BEDTools: a powerful toolset for genome arithmetic. 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, bgen/4.1.3 A BGEN file format reader. It fully supports the BGEN format specifications 1.2 and 1.3. 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 bio-searchio-hmmer: bio-searchio-hmmer/1.7.3 Code to parse output from hmmsearch, hmmscan, phmmer and nhmmer, compatible with both version 2 and version 3 of the HMMER package from http://hmmer.org. bioawk: bioawk/1.0 Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names. 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/1.7.8 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 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 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, blast+/2.11.0, blast+/2.12.0, ... 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. blender: blender/3.1.2-linux-x64 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. blis: blis/0.6.0, blis/0.8.1 BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries. blosc: blosc/1.17.1 Blosc, an extremely fast, multi-threaded, meta-compressor library bmtagger: bmtagger/3.101 Best Match Tagger for removing human reads from metagenomics datasets bmvdgeijn-wasp: bmvdgeijn-wasp/0.3.4-python-3.7.4 WASP is a suite of tools for unbiased allele-specific read mapping and discovery of molecular QTLs. 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 provides free peer-reviewed portable C++ source libraries. boost.python: boost.python/1.71.0-python-2.7.16, ... 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, bowtie2/2.4.2 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. bpipe: bpipe/0.9.9.7 Bpipe - a tool for running and managing bioinformatics pipelines bracken: bracken/2.6.0 Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. Braken uses the taxonomy labels assigned by Kraken, a highly accurate metagenomics classification algorithm, to estimate the number of reads originating from each species present in a sample. Kraken classifies reads to the best matching location in the taxonomic tree, but does not estimate abundances of species. We use the Kraken database itself to derive probabilities that describe how much sequence from each genome is identical to other genomes in the database, and combine this information with the assignments for a particular sample to estimate abundance at the species level, the genus level, or above. Combined with the Kraken classifier, Bracken produces accurate species- and genus-level abundance estimates even when a sample contains two or more near-identical species. NOTE: Bracken is compatible with both Kraken 1 and Kraken 2. However, the default kmer length is different depending on the version of Kraken used. If you use Kraken 1 defaults, specify 31 as the kmer length. If you use Kraken 2 defaults, specify 35 as the kmer length. brotli: brotli/1.0.9 Brotli is a generic-purpose lossless compression algorithm that compresses data using a combination of a modern variant of the LZ77 algorithm, Huffman coding and 2nd order context modeling, with a compression ratio comparable to the best currently available general-purpose compression methods. It is similar in speed with deflate but offers more dense compression. The specification of the Brotli Compressed Data Format is defined in RFC 7932. bsddb3: bsddb3/6.2.6, bsddb3/6.2.9 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. 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-mem2: bwa-mem2/2.2.1 Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. bwa-meth: bwa-meth/0.2.2 Fast and accurante alignment of BS-Seq reads. bx-python: bx-python/0.8.4, bx-python/0.8.9-python-3.8.6 The bx-python project is a Python library and associated set of scripts to allow for rapid implementation of genome scale analyses. 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, capnproto/0.9.1 Cap’n Proto is an insanely fast data interchange format and capability-based RPC system. cat: cat/5.2.3 CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs) cbc: cbc/2.10.5 Cbc (Coin-or branch and cut) is an open-source mixed integer linear programming solver written in C++. It can be used as a callable library or using a stand-alone executable. 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/1.9.10 CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data. cellranger: cellranger/3.1.0, cellranger/6.1.1, cellranger/7.0.0 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 cesm: cesm/2.1.3 CESM is a fully-coupled, community, global climate model that provides state-of-the-art computer simulations of the Earth's past, present, and future climate states. cfdemcoupling: cfdemcoupling/3.8.0 CFDEMcoupling is an open source CFD-DEM engine. It provides the possibility to couple the DEM engine LIGGGHTS to a CFD framework. cfitsio: cfitsio/3.47, cfitsio/3.48, cfitsio/3.49 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, ... 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. cgl: cgl/0.60.3 The COIN-OR Cut Generation Library (Cgl) is a collection of cut generators that can be used with other COIN-OR packages that make use of cuts, such as, among others, the linear solver Clp or the mixed integer linear programming solvers Cbc or BCP. Cgl uses the abstract class OsiSolverInterface (see Osi) to use or communicate with a solver. It does not directly call a solver. 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/2.2.0 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/1.0.18-python-2.7.18, 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. chemtrayzer: chemtrayzer/2.1 ChemTraYzer creates reaction models from molecular dynamics simulations. It's available as open software (MIT license). Please find a full description @ https://www.ltt.rwth-aachen.de/cms/LTT/Forschung/Forschung-am-LTT/Model-Based-Fuel-Design/Aktuelle-Projekte/~kqbf/ChemTraYzer/lidx/1 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/9.0.1-cuda-10.1.243, clang/10.0.0, clang/11.0.1 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 clp: clp/1.17.7 Clp (Coin-or linear programming) is an open-source linear programming solver. It is primarily meant to be used as a callable library, but a basic, stand-alone executable version is also available. 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/3.20.1, ... CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software. cmake-gui: cmake-gui/3.18.4 CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software. cnvcaller: cnvcaller/20181210 cnvnator: cnvnator/0.4.1 a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads code-server: code-server/4.8.3 Run VS Code on any machine anywhere and access it in the browser. coinutils: coinutils/2.11.4 CoinUtils (Coin-OR Utilities) is an open-source collection of classes and functions that are generally useful to more than one COIN-OR project. combined-pvalues: combined-pvalues/0.50.6 library to combine, analyze, group and correct p-values in BED files. Unique tools involve correction for spatial autocorrelation. This is useful for ChIP-Seq probes and Tiling arrays, or any data with spatial correlation. comsol: comsol/5.5, comsol/5.6, comsol/6.0 COMSOL is a cross-platform finite element analysis, solver adn multipyhsics simulation software concoct: concoct/1.1.0-python-2.7.18 Clustering cONtigs with COverage and ComposiTion (CONCOCT) is a program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads. connectomeworkbench: connectomeworkbench/1.4.2, connectomeworkbench/1.5.0 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. coverm: coverm/0.6.1-linux-x86_64 CoverM aims to be a configurable, easy to use and fast DNA read coverage and relative abundance calculator focused on metagenomics applications. cplex: cplex/12.8, cplex/12.10-python-3.7.4 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. crest: crest/2.11 CREST is an utility/driver program for the xtb program. Originally it was designed as conformer sampling program, hence the abbreviation Conformer–Rotamer Ensemble Sampling Tool, but now offers also some utility functions for calculations with the GFNn–xTB methods. Generally the program functions as an IO based OMP scheduler (i.e., calculations are performed by the xtb program) and tool for the creation and analysation of structure ensembles. cromwell: cromwell/51-java-11.0.2 Cromwell is a Workflow Management System geared towards scientific workflows. csvtk: csvtk/0.25.0 A cross-platform, efficient and practical CSV/TSV toolkit in Golang ctffind: ctffind/4.1.14 Program for finding CTFs of electron micrographs. cuda: cuda/8.0.61, cuda/10.1.243, cuda/10.2.89, cuda/11.1.1, cuda/11.3.1, ... 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/11.0.2, cudacore/11.1.1, cudacore/11.2.1 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, ... 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, curl/7.76.0, curl/7.78.0 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/1.18-python-2.7.18, 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/0.29.22, cython/0.29.24, ... 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. das_tool: das_tool/1.1.3-r-4.0.4-python-2.7.18 DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly. dashing: dashing/1.0 Dashing sketches and computes distances between fasta and fastq data. 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/18.1.32, 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, db_file/1.855 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, dbus/1.13.18 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/3.6.6 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. demuxlet: demuxlet/11022021 Genetic multiplexing of barcoded single cell RNA-seq dendropy: dendropy/4.4.0, dendropy/4.5.2-python-2.7.18, dendropy/4.5.2 A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters. deploid: deploid/0.6-beta.2 dEploid is designed for deconvoluting mixed genomes with unknown proportions. Traditional ‘phasing’ programs are limited to diploid organisms diamond: diamond/0.9.30, diamond/2.0.6, diamond/2.0.7 Accelerated BLAST compatible local sequence aligner dmd: dmd/2.100.0 D is a general-purpose programming language with static typing, systems-level access, and C-like syntax. With the D Programming Language, write fast, read fast, and run fast. dmtcp: dmtcp/2.6.0, dmtcp/3.0.0 DMTCP is a tool to transparently checkpoint the state of multiple simultaneous applications, including multi-threaded and distributed applications. It operates directly on the user binary executable, without any Linux kernel modules or other kernel modifications. 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, double-conversion/3.1.5 Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles. doxygen: doxygen/1.8.16, doxygen/1.8.20, doxygen/1.9.1 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. ea-utils: ea-utils/20220218 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. eagle: eagle/1.1.3 Explicit Alternative Genome Likelihood Evaluator 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/2.17.0 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). edlib: edlib/1.3.9 Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance. eeglab: eeglab/2020.0 EEGLAB is an open source signal processing environment for electrophysiological signals running on Matlab and developed at the SCCN/UCSD 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/3.3.9 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. elfutils: elfutils/0.183, elfutils/0.185 The elfutils project provides libraries and tools for ELF files and DWARF data. elpa: elpa/2019.11.001 Eigenvalue SoLvers for Petaflop-Applications . emacs: emacs/26.3, emacs/27.1 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, ... 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. epacts: epacts/3.3.2 EPACTS is a versatile software pipeline to perform various statistical tests for identifying genome-wide association from sequence data through a user-friendly interface, both to scientific analysts and to method developers. 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, exiv2/0.27.4 Exiv2 is a Cross-platform C++ library and a command line utility to manage image metadata. expat: expat/2.2.7, expat/2.2.9, expat/2.4.1 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) expecttest: expecttest/0.1.3 This library implements expect tests (also known as "golden" tests). Expect tests are a method of writing tests where instead of hard-coding the expected output of a test, you run the test to get the output, and the test framework automatically populates the expected output. If the output of the test changes, you can rerun the test with the environment variable EXPECTTEST_ACCEPT=1 to automatically update the expected output. eyeeeg: eyeeeg/0.4.1 EYE-EEG toolbox for combining eye-tracking and EEG 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/1.33 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. fastbdt: fastbdt/5.2 A speed-optimized and cache-friendly implementation of stochastic gradient-boosted decision trees for multivariate classification fastgear: fastgear/20161216 Inference of recent and ancestral recombination between divergent lineages in bacteria. fastp: fastp/0.20.0, fastp/0.23.2 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 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/2.1.11 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, fds/6.7.9 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/3.3.9, fftw/3.3.10 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 flac: flac/1.3.3 FLAC stands for Free Lossless Audio Codec, an audio format similar to MP3, but lossless, meaning that audio is compressed in FLAC without any loss in quality. 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. flashpca: flashpca/2.0 FlashPCA performs fast principal component analysis (PCA) of single nucleotide polymorphism (SNP) data, similar to smartpca from EIGENSOFT (http://www.hsph.harvard.edu/alkes-price/software/) and shellfish (https://github.com/dandavison/shellfish). flatbuffers: flatbuffers/1.12.0, flatbuffers/2.0.0 FlatBuffers: Memory Efficient Serialization Library flatbuffers-python: flatbuffers-python/1.12, flatbuffers-python/2.0 Python Flatbuffers runtime 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. flexiblas: flexiblas/3.0.4 FlexiBLAS is a wrapper library that enables the exchange of the BLAS and LAPACK implementation used by a program without recompiling or relinking it. 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/2.9 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/2.13.93, ... Fontconfig is a library designed to provide system-wide font configuration, customization and application access. foss: foss/2019b, foss/2020b, foss/2021a, foss/2021b 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. fpc: fpc/3.2.2 Free Pascal is a mature, versatile, open source Pascal compiler. 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. freefem: freefem/4.11-python-3.7.4 FreeFEM offers a fast interpolation algorithm and a language for the manipulation of data on multiple meshes. freeglut: freeglut/3.0.0-mesa18, freeglut/3.0.0-mesa19, freeglut/3.0.0, ... freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library. freeimage: freeimage/3.18.0 FreeImage is an Open Source library project for developers who would like to support popular graphics image formats like PNG, BMP, JPEG, TIFF and others as needed by today's multimedia applications. FreeImage is easy to use, fast, multithreading safe. freesurfer: freesurfer/6.0.1-centos6_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/2.10.4, ... 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/6.0.5.1 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. g_mmpbsa: g_mmpbsa/2016 MM/PBSA method for GROMACS 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. gawk: gawk/5.1.1 The awk utility interprets a special-purpose programming language that makes it possible to handle simple data-reformatting jobs with just a few lines of code. gc: gc/7.6.12, gc/8.0.4 The Boehm-Demers-Weiser conservative garbage collector can be used as a garbage collecting replacement for C malloc or C++ new. gcc: 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, ... 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. gcta: gcta/1.94.0beta GCTA (Genome-wide Complex Trait Analysis) is a software package, which was initially developed to estimate the proportion of phenotypic variance explained by all genome-wide SNPs for a complex trait but has been extensively extended for many other analyses of data from genome-wide association studies (GWASs). 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/3.2.1-python-3.8.6, gdal/3.3.2 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, gdb/10.1 The GNU Project Debugger gdk-pixbuf: gdk-pixbuf/2.38.2, gdk-pixbuf/2.40.0 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. gdrcopy: gdrcopy/2.0, gdrcopy/2.2, gdrcopy/2.3 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. gegl: gegl/0.3.34, gegl/0.4.30 GEGL (Generic Graphics Library) is a data flow based image processing framework, providing floating point processing and non-destructive image processing capabilities to GNU Image Manipulation Program (GIMP) and other projects. gencore: gencore/0.13.0 An efficient tool to remove sequencing duplications and eliminate sequencing errors by generating consensus reads. genometools: genometools/1.6.1 A comprehensive software library for efficient processing of structured genome annotations. genozip: genozip/13.0.12 Genozip is a compressor for BAM, FASTQ, VCF and other genomic files. Documentation: genozip.com. Support: support@genozip.com 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/3.9.1 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). gffread: gffread/0.12.7 GFF/GTF parsing utility providing format conversions, region filtering, FASTA sequence extraction and more. 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/9.53.3, ... 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/2.28.0-nodocs, git/2.33.1-nodocs, ... 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/3.1.14 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-mesa20, ... GL2PS: an OpenGL to PostScript printing library glib: glib/2.62.0, glib/2.66.1, glib/2.68.2, glib/2.69.1 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, glm/0.9.9.8 OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics software based on the OpenGL Shading Language (GLSL) specifications. globalarrays: globalarrays/5.7.2 Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model glog: glog/0.3.5, glog/0.4.0, glog/0.5.0 A C++ implementation of the Google logging module. glpk: glpk/4.65, glpk/5.0 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/6.2.1 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, gnuplot/5.4.1 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/1.17.3, go/1.17.6 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 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, gompi/2021a, gompi/2021b 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/2.9.1 gperftools is a collection of a high-performance multi-threaded malloc() implementation, plus some pretty nifty performance analysis tools. Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler. gradunwarp: gradunwarp/1.2.0-hcp-python-3.7.4 Gradient Unwarping. This is the Human Connectome Project fork of the no longer maintained original. graphicsmagick: graphicsmagick/1.3.31, graphicsmagick/1.3.34, ... GraphicsMagick is the swiss army knife of image processing. graphmap: graphmap/0.5.2 A highly sensitive and accurate mapper for long, error-prone reads graphmap2: graphmap2/0.6.4 A highly sensitive and accurate mapper for long, error-prone reads graphviz: graphviz/2.42.2-python-3.7.4, ... 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. 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 gridss: gridss/2.11.1 GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements. . 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 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 builds. It also contains the gmxapi extension for the single precision MPI build. gsl: gsl/2.5, gsl/2.6, gsl/2.7 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, gst-plugins-base/1.16.2 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/1.16.2 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, gtdb-tk/1.7.0-python-3.8.6, ... A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes. gtk+: gtk+/3.24.8, gtk+/3.24.13, gtk+/3.24.23 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/3.1.2 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. 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/2.2.6, 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/5.0.11, guppy/5.0.14 Guppy software supports MinIT and MinION instruments from Nanopore Technologies gurobi: gurobi/9.0.0, gurobi/9.0.3, gurobi/10.0.1-python-3.7.4, ... 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, h5py/3.1.0, h5py/3.6.0 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/2.6.7, harfbuzz/2.8.1, ... 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-no-netcdf, hdf/4.2.14, hdf/4.2.15 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, hdf5/1.8.20, hdf5/1.10.5-nompi, hdf5/1.10.5-test, ... 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. healpix: healpix/3.82 Hierarchical Equal Area isoLatitude Pixelation of a sphere. 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 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. hic-pro: hic-pro/3.0.0-python-3.8.6 HiC-Pro was designed to process Hi-C data, from raw fastq files (paired-end Illumina data) to the normalized contact maps. hifiasm: hifiasm/0.16.1 Hifiasm is a fast haplotype-resolved de novo assembler for PacBio HiFi reads. It can assemble a human genome in several hours and assemble a ~30Gb California redwood genome in a few days. 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 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/1.11, htslib/1.12, htslib/1.14, ... 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, hwloc/2.4.1, hwloc/2.5.0 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 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/2.24.0 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. 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, ... 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 iced: iced/0.5.10 The python module iced implements the ICE normalization of hic data. icu: icu/64.2, icu/65.1, icu/67.1, icu/69.1 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 imake: imake/1.0.8 imake is a Makefile-generator that is intended to make it easier to develop software portably for multiple systems. imkl: imkl/2017.2.174, imkl/2019.5.281, imkl/2020.4.304 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. imod: imod/4.11.5 IMOD is a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections. The package contains tools for assembling and aligning data within multiple types and sizes of image stacks, viewing 3-D data from any orientation, and modeling and display of the image files. IMOD was developed primarily by David Mastronarde, Rick Gaudette, Sue Held, Jim Kremer, Quanren Xiong, and John Heumann at the University of Colorado. impute2: impute2/2.3.2_x86_64_dynamic, impute2/2.3.2_x86_64_static IMPUTE version 2 (also known as IMPUTE2) is a genotype imputation and haplotype phasing program based on ideas from Howie et al. 2009 infernal: infernal/1.1.4 Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. inline: inline/0.3.19-r-4.0.4 Functionality to dynamically define R functions and S4 methods with 'inlined' C, C++ or Fortran code supporting the .C and .Call calling conventions. 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. interproscan: interproscan/5.59-91.0, interproscan/5.60-92.0 InterProScan is a sequence analysis application (nucleotide and protein sequences) that combines different protein signature recognition methods into one resource. intervaltree-python: intervaltree-python/3.1.0 A mutable, self-balancing interval tree. Queries may be by point, by range overlap, or by range containment. 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. ipopt: ipopt/3.12.13, ipopt/3.14.4 IPOPT (Interior Point Optimizer, pronounced Eye-Pea-Opt) is an open source software package for large-scale nonlinear optimization. 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 irfinder: irfinder/1.3.1, irfinder/2.0.1 IRFinder detects intron retention from RNA-Seq experiments. isa-l: isa-l/2.30.0 Intelligent Storage Acceleration Library isl: isl/0.23 isl is a library for manipulating sets and relations of integer points bounded by linear constraints. itk: itk/5.2.1 Insight Segmentation and Registration Toolkit (ITK) provides an extensive suite of software tools for registering and segmenting multidimensional imaging data. ivar: ivar/1.3.1 iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing. 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 jansson: jansson/2.13.1 Jansson is a C library for encoding, decoding and manipulating JSON data. Its main features and design principles are: * Simple and intuitive API and data model * Comprehensive documentation * No dependencies on other libraries * Full Unicode support (UTF-8) * Extensive test suite jasper: jasper/2.0.14, jasper/2.0.24, jasper/2.0.33 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/1.7.0_80, java/1.8.0_241, java/11.0.2, java/13.0.2, ... Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers. jbigkit: jbigkit/2.1 JBIG-KIT is a software implementation of the JBIG1 data compression standard (ITU-T T.82), which was designed for bi-level image data, such as scanned documents. 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. jq: jq/1.5 jq is a lightweight and flexible command-line JSON processor. json-c: json-c/0.15 JSON-C implements a reference counting object model that allows you to easily construct JSON objects in C, output them as JSON formatted strings and parse JSON formatted strings back into the C representation of JSON objects. json-glib: json-glib/1.6.2 JSON-GLib implements a full JSON parser and generator using GLib and GObject, and integrates JSON with GLib data types. jsoncpp: jsoncpp/1.9.3, jsoncpp/1.9.4 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 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-2.7.16, 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/2.3.1-python-3.7.4, ... Keras is a deep learning API written in Python, running on top of the machine learning platform TensorFlow. kim-api: kim-api/2.1.3, kim-api/2.2.1 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. kma: kma/1.3.22 KMA is a mapping method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend. 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/1.1.1 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. Prebuilt databases can be found at /data/gpfs/databases/KRAKEN kraken2: kraken2/2.0.8-beta-perl-5.30.0, kraken2/2.1.2-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. Prebuilt databases can be found at /data/gpfs/databases/KRAKEN2 kronatools: kronatools/2.7.1, kronatools/2.8 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 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/3.9.1 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. last: last/1066, last/1179 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. leptonica: leptonica/1.82.0 Leptonica is a collection of pedagogically-oriented open source software that is broadly useful for image processing and image analysis applications. 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. lftp: lftp/4.9.2 LFTP is a sophisticated ftp/http client, and a file transfer program supporting a number of network protocols. Like BASH, it has job control and uses the readline library for input. It has bookmarks, a built-in mirror command, and can transfer several files in parallel. It was designed with reliability in mind. libaio: libaio/0.3.111, libaio/0.3.112 Asynchronous input/output library that uses the kernels native interface. libarchive: libarchive/3.4.3, libarchive/3.5.1 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/1.14 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, libdap/3.20.7 A C++ SDK which contains an implementation of DAP 2.0 and DAP4.0. This includes both Client- and Server-side support classes. libdeflate: libdeflate/1.8 Heavily optimized library for DEFLATE/zlib/gzip compression and decompression. libdrm: libdrm/2.4.99, libdrm/2.4.102, libdrm/2.4.106, libdrm/2.4.107 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, libffcall/2.4 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, libffi/3.4.2 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, libgcrypt/1.8.5 Libgpg-error is a small library that defines common error values for all GnuPG components. libgd: libgd/2.2.5, libgd/2.3.0, libgd/2.3.1 GD is an open source code library for the dynamic creation of images by programmers. libgeotiff: libgeotiff/1.5.1, libgeotiff/1.6.0, libgeotiff/1.7.0 Library for reading and writing coordinate system information from/to GeoTIFF files libgit2: libgit2/1.1.1 libgit2 is a portable, pure C implementation of the Git core methods provided as a re-entrant linkable library with a solid API, allowing you to write native speed custom Git applications in any language which supports C bindings. libglu: libglu/9.0.0, libglu/9.0.1, libglu/9.0.2 The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. libglvnd: libglvnd/1.2.0, libglvnd/1.3.2, libglvnd/1.3.3 libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors. libgpg-error: libgpg-error/1.36, libgpg-error/1.38 Libgpg-error is a small library that defines common error values for all GnuPG components. libgpuarray: libgpuarray/0.7.6-python-3.7.4, ... Library to manipulate tensors on the GPU. libharu: libharu/2.3.0 libHaru is a free, cross platform, open source library for generating PDF files. libice: libice/1.0.10 X Inter-Client Exchange library for freedesktop.org libiconv: libiconv/1.16 Libiconv converts from one character encoding to another through Unicode conversion libidn: libidn/1.35, libidn/1.36 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. libidn2: libidn2/2.3.0 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. libint: libint/1.1.6 Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory. 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. libmypaint: libmypaint/1.3.0, libmypaint/1.6.1 libmypaint, a.k.a. "brushlib", is a library for making brushstrokes which is used by MyPaint and other projects libogg: libogg/1.3.4, libogg/1.3.5 Ogg is a multimedia container format, and the native file and stream format for the Xiph.org multimedia codecs. 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, libreadline/8.1 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, libsigsegv/2.13 GNU libsigsegv is a library for handling page faults in user mode. libsm: libsm/1.2.3 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. libsndfile: libsndfile/1.0.28, libsndfile/1.0.31 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/2.70.0 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, libtasn1/4.16.0 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, libtiff/4.2.0, libtiff/4.3.0 tiff: Library and tools for reading and writing TIFF data files libtirpc: libtirpc/1.1.4, libtirpc/1.3.1, libtirpc/1.3.2 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, libunwind/1.4.0, libunwind/1.5.0 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 libuuid: libuuid/1.0.3 Portable uuid C library libvips: libvips/8.11.2 libvips is a demand-driven, horizontally threaded image processing library. libvorbis: libvorbis/1.3.7 Ogg Vorbis is a fully open, non-proprietary, patent-and-royalty-free, general-purpose compressed audio format libwebp: libwebp/1.0.2, libwebp/1.1.0, libwebp/1.2.0 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. libxaw: libxaw/1.0.13 libXaw provides the Athena Widgets toolkit 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). libxmu: libxmu/1.1.3 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 libxpm: libxpm/3.5.13 libXp provides the X print library. libxrender: libxrender/0.9.9 X11 client-side library libxslt: libxslt/1.1.33, libxslt/1.1.34 Libxslt is the XSLT C library developed for the GNOME project (but usable outside of the Gnome platform). libxsmm: libxsmm/1.16.1 LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86). libxt: libxt/1.2.0 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). 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, littlecms/2.11, littlecms/2.12 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, llvm/11.0.0, llvm/11.1.0, ... 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/0.9.29 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. longshot: longshot/0.4.3 Longshot is a variant calling tool for diploid genomes using long error prone reads such as Pacific Biosciences (PacBio) SMRT and Oxford Nanopore Technologies (ONT). It takes as input an aligned BAM file and outputs a phased VCF file with variants and haplotype information. It can also output haplotype-separated BAM files that can be used for downstream analysis. Currently, it only calls single nucleotide variants (SNVs). lpsolve: lpsolve/5.5.2.5, lpsolve/5.5.2.11 Mixed Integer Linear Programming (MILP) solver lua: lua/5.1.5, lua/5.4.2 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. lynx: lynx/2.8.7 lynx is an alphanumeric display oriented World-Wide Web Client lz4: lz4/1.9.2, lz4/1.9.3 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, m4/1.4.19 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. make: make/4.3 GNU version of make utility makedepend: makedepend/1.0.6 The makedepend package contains a C-preprocessor like utility to determine build-time dependencies. makeinfo: makeinfo/6.7-minimal, makeinfo/6.7 makeinfo is part of the Texinfo project, the official documentation format of the GNU project. mako: mako/1.1.0, mako/1.1.3-python-3.8.6, mako/1.1.4 A super-fast templating language that borrows the best ideas from the existing templating languages mambaforge: mambaforge/4.12.0 Mambaforge is based on miniforge and allows you to install the conda package manager with the following features pre-configured: conda-forge set as the default (and only) channel, and support for Mamba in place of Conda. manta: manta/1.6.0-python-2.7.16 Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. mapdamage: mapdamage/2.2.1-r-4.0.4-python3.8.6 mapDamage2 is a computational framework written in Python and R, which tracks and quantifies DNA damage patterns among ancient DNA sequencing reads generated by Next-Generation Sequencing platforms. 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, mash/2.3 Fast genome and metagenome distance estimation using MinHash masurca: masurca/3.4.2, masurca/4.0.1, masurca/4.0.5 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/1.5.21 matio is an C library for reading and writing Matlab MAT files. matlab: matlab/2019a, matlab/2019b, matlab/2020a-update5, matlab/2020a, ... 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 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/2.2.7 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, mcr/r2017b 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, medaka/1.6.0 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. mediaflux-explorer: mediaflux-explorer/current mediaflux-explorer is a Java-based GUI application focusing uploads, downloads, queries and sharing of data. 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/1.1.4-python-2.7.16, megahit/1.1.4-python-3.7.4, ... 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, meme/5.4.1-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/20.2.1, mesa/21.1.1, ... 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/0.58.0, ... Meson is a cross-platform build system designed to be both as fast and as user friendly as possible. meta: meta/1.7 META is a program for the meta analysis of genome-wide association studies. The program is designed to synthesizing the evidence from different association studies. Particularly, the program is able to work seamlessly with the output of SNPTEST. metabat: metabat/2.12.1-python-2.7.16, metabat/2.15-python-2.7.18 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 metaphlan2: metaphlan2/2.7.8-python-3.7.4 MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. With the newly added StrainPhlAn module, it is now possible to perform accurate strain-level microbial profiling. metavelvet: metavelvet/1.2.02 A short read assember for metagenomics metawrap: metawrap/1.3-python-2.7.18 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. 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. minia: minia/3.2.6 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. 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, miniconda3/4.9.2 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, minimap2/2.18, minimap2/2.20, ... 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 mixcr: mixcr/3.0.13-java-1.8.0_241 MiXCR processes big immunome data from raw sequences to quantitated clonotypes mixer: mixer/1.2 Causal Mixture Model for GWAS summary statistics mlst: mlst/2.16 Scan contig files against traditional PubMLST typing schemes. mmseqs2: mmseqs2/13-45111 MMseqs2: ultra fast and sensitive search and clustering suite molmod: molmod/1.4.5-python-2.7.16, 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, mono/6.8.0.105, mono/6.12.0.122 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. mpc: mpc/1.2.1 Gnu Mpc is a C library for the arithmetic of complex numbers with arbitrarily high precision and correct rounding of the result. It extends the principles of the IEEE-754 standard for fixed precision real floating point numbers to complex numbers, providing well-defined semantics for every operation. At the same time, speed of operation at high precision is a major design goal. 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/3.4.2, mpich/3.4.3 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. msm: msm/3.0 Multimodal Surface Matching with Higher order Clique Reduction msmc2: msmc2/2.1.3 This program implements MSMC2, a method to infer population size history and population separation history from whole genome sequencing data 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, multiwell/2021 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-seq, mumps/5.2.1-metis, mumps/5.3.5-metis-seq, ... 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-sigma-scale, namd/2.14-mpi-standard-rest2, ... NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. nanocount: nanocount/1.0.0.post6-python-3.8.2 NanoCount estimates transcripts abundance from Oxford Nanopore direct-RNA sequencing datasets, using an expectation-maximization approach like RSEM, Kallisto, salmon, etc to handle the uncertainty of multi-mapping reads 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, ... 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-r-4.0.4 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/4.7.4, netcdf/4.8.1 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-c++4/4.3.1 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/4.4.5, 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, ... 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/3.6, nettle/3.7.3 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/2.5-python-3.8.6, ... 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. nextflow: nextflow/21.04.2, nextflow/21.08.0, nextflow/22.04.5 Nextflow is a reactive workflow framework and a programming DSL that eases writing computational pipelines with complex data ngs: ngs/2.9.3-java-11.0.2, ngs/2.10.9 NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. ngsadmix: ngsadmix/32 NGSadmix is a tool for finding admixture proportions from NGS data, based on genotype likelihoods. 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/1.4.6 Nim is a systems and applications programming language. ninja: ninja/1.9.0, ninja/1.10.1-python-3.8.6, ninja/1.10.1, ninja/1.10.2 Ninja is a small build system with a focus on speed. nlopt: nlopt/2.6.1, nlopt/2.6.2, nlopt/2.7.0 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/12.19.0, nodejs/12.21.0, nodejs/14.17.6 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. nsight-systems: nsight-systems/2022.2.1 NVIDIA® Nsight™ Systems is a system-wide performance analysis tool designed to visualize an application’s algorithm, help you select the largest opportunities to optimize, and tune to scale efficiently across any quantity of CPUs and GPUs in your computer; from laptops to DGX servers. nspr: nspr/4.21, nspr/4.29 Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level and libc-like functions. nss: nss/3.45, nss/3.57 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, numactl/2.0.14 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/0.53.1 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. numexpr: numexpr/2.7.1-python-3.7.4 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-python-2.7.16, numpy/1.9.2-python-2.7.16, ... 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. nvhpc: nvhpc/21.9, nvhpc/22.2, nvhpc/22.7 C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI) octave: octave/4.2.1, octave/5.2.0, octave/6.2.0 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. ont-fast5-api: ont-fast5-api/4.0.2 ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore .fast5 file format. openai-gym: openai-gym/0.17.1-python-3.7.4 A toolkit for developing and comparing reinforcement learning algorithms. openbabel: openbabel/2.4.1-python-2.7.16, openbabel/2.4.1-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/0.3.15, ... 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 (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. Includes extra modules for OpenCV from the contrib repository. openexr: openexr/2.5.5 OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic for use in computer imaging applications openfast: openfast/2.3.0 OpenFAST is a wind turbine simulation tool which builds on FAST v8. openfoam: openfoam/v1906, openfoam/v1912, openfoam/v2106, ... 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/2.4.0 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. openmm: openmm/7.5.1 OpenMM is a toolkit for molecular simulation. openmolcas: openmolcas/21.06 OpenMolcas is a quantum chemistry software package openmpi: openmpi/3.1.4, openmpi/3.1.6, ... 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, openssl/1.1.1f, openssl/1.1.1h, openssl/1.1.1k 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. opera-ms: opera-ms/0.9.0-20200802-python-3.7.4, ... 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. optix: optix/6.5.0, optix/7.1.0, optix/7.6.0 OptiX is NVIDIA SDK for easy ray tracing performance. It provides a simple framework for accessing the GPU’s massive ray tracing power using state-of-the-art GPU algorithms. orca: orca/4.2.1, orca/5.0.1-static, orca/5.0.1, orca/5.0.2, orca/5.0.3 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/2.5.4 OrthoFinder: phylogenetic orthology inference for comparative genomics osi: osi/0.108.6 Osi (Open Solver Interface) provides an abstract base class to a generic linear programming (LP) solver, along with derived classes for specific solvers. Many applications may be able to use the Osi to insulate themselves from a specific LP solver. That is, programs written to the OSI standard may be linked to any solver with an OSI interface and should produce correct results. The OSI has been significantly extended compared to its first incarnation. Currently, the OSI supports linear programming solvers and has rudimentary support for integer programming. 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/1.47.0, ... 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. papi: papi/5.7.0, papi/6.0.0 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/20210322 parallel: Build and execute shell commands in parallel parasail: parasail/2.5 parasail is a SIMD C (C99) library containing implementations of the Smith-Waterman (local), Needleman-Wunsch (global), and semi-global pairwise sequence alignment algorithms. paraview: paraview/5.2.0-python-2.7.16-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-python-3.7.4 Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. pasapipeline: pasapipeline/2.4.1 Program for analysing NGS data. patchelf: patchelf/0.10, patchelf/0.12 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. pcangsd: pcangsd/1.10-python-3.8.6, pcangsd/1.11-python-3.8.6 Framework for analyzing low-depth next-generation sequencing (NGS) data in heterogeneous/structured populations using principal component analysis (PCA). 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, pcre/8.44, pcre/8.45 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, pcre2/10.35, pcre2/10.36, pcre2/10.37 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/5.28.1, perl/5.30.0, perl/5.32.0-minimal, perl/5.32.0, ... Larry Wall's Practical Extraction and Report Language This is a minimal build without any modules. Should only be used for build dependencies. pest: pest/15 Model-Independent Parameter Estimation and Uncertainty Analysis petsc: petsc/3.11.0-downloaded-deps, petsc/3.12.4, petsc/3.18.1 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. pftoolsv3: pftoolsv3/3.2.11 A suite of tools to build and search generalized profiles (protein and DNA). 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, picard/2.25.0-java-11 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/2.6 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 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-simd/7.1.2 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 pip: pip/21.2.4-python-3.7.4, pip/21.2.4-python-3.8.6, ... pip is the package installer for Python. You can use pip to install packages from the Python Package Index and other indexes.. 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/0.40.0 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). pkgconf: pkgconf/1.9.3 pkgconf is a program which helps to configure compiler and linker flags for development libraries. It is similar to pkg-config from freedesktop.org. pkgconfig: pkgconfig/1.5.1-python, 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-2.7.16, ... 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, pmix/3.2.3 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, pnetcdf/1.12.1 Parallel netCDF: A Parallel I/O Library for NetCDF File Access pocl: pocl/1.4, pocl/1.6 Pocl is a portable open source (MIT-licensed) implementation of the OpenCL standard polspice: polspice/3.7.5 PolSpice (aka Spice) is a tool to statistically analyze Cosmic Microwave Background (CMB) data, as well as any other diffuse data pixelized on the sphere. 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 postgresql: postgresql/13.2, postgresql/13.4 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. pov-ray: pov-ray/3.7.0.8 The Persistence of Vision Raytracer, or POV-Ray, is a ray tracing program which generates images from a text-based scene description, and is available for a variety of computer platforms. POV-Ray is a high-quality, Free Software tool for creating stunning three-dimensional graphics. The source code is available for those wanting to do their own ports. 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. prinseq: prinseq/0.20.4-perl-5.30.0 A bioinformatics tool to PRe-process and show INformation of SEQuence data. 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. prodigal-gv: prodigal-gv/2.9.0 A fork of Prodigal meant to improve gene calling for giant viruses and viruses that use alternative genetic codes. proj: proj/4.9.3, proj/5.2.0, proj/6.2.1, proj/7.2.1, proj/8.1.0, ... 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. proot: proot/5.1.1 PRoot is a user-space implementation of chroot, mount --bind, and binfmt_misc. protobuf: protobuf/3.7.1, protobuf/3.10.0, protobuf/3.12.3, ... Google Protocol Buffers protobuf-python: protobuf-python/3.10.0-python-3.7.4, ... 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/1.11 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. pullseq: pullseq/1.0.2 Utility program for extracting sequences from a fasta/fastq file puremd: puremd/20210427 PuReMD is our implementation of reactive molecular dynamics using ReaxFF force field. PuReMD and its incorporation in LAMMPS (Reax/C) is used by large number of research groups worldwide for simulating diverse systems ranging from biomembranes to explosives (RDX) at atomistic level of detail. pybedtools: pybedtools/0.8.1-python-3.7.4 pybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python. pybind11: pybind11/2.4.3-python-3.7.4, pybind11/2.6.0-python-3.8.2, ... 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 pyfaidx: pyfaidx/0.7.0 pyfaidx: efficient pythonic random access to fasta subsequences pylint: pylint/2.2.3-python-3.7.4 Pylint is a tool that checks for errors in Python code, tries to enforce a coding standard and looks for code smells. It can also look for certain type errors, it can recommend suggestions about how particular blocks can be refactored and can offer you details about the code's complexity. 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/0.16.0.1-python-2.7.18, ... 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 pyspoa: pyspoa/0.0.8 Python bindings to spoa. pytables: pytables/3.6.1-python-3.7.4 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. pytest: pytest/6.0.1-python-3.7.4, pytest/6.0.1-python-3.8.2 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/2.7.18, python/3.7.4, python/3.8.2, ... 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). python-isal: python-isal/0.11.1 Faster zlib and gzip compatible compression and decompression by providing python bindings for the isa-l library. python-parasail: python-parasail/1.2.4 Python Bindings for the Parasail C Library pytorch: pytorch/1.4.0-python-3.7.4, pytorch/1.5.1-python-3.7.4, ... 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/5.3.1 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. . qes-winds: qes-winds/1.0 QES-Winds is a fast response 3D diagnostic urban wind model written in C++ and uses NVIDIA's CUDA framework to accelerate a mass-conserving wind-field solver. qhull: qhull/2015.2, qhull/2019.1, qhull/2020.2 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, qiime2/2021.8 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, qt5/5.14.2-temp, qt5/5.14.2 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-2.7.18, 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. quickld: quickld/0.2.3 quickLD (qLD) is a tool to calculate Linkage disequilibrium (the non-random association between alleles at different loci), with highly efficient CPU and GPU kernels that utilize dense linear algebra (DLA) operations. Further information behind this software can be found in the related publications below.. quickmerge: quickmerge/0.3 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/4.0.4, r/4.0.5-bare, r/4.0.5, r/4.1.0, ... R is a free software environment for statistical computing and graphics. r-bundle-bioconductor: r-bundle-bioconductor/3.9-r-3.6.0, ... Bioconductor provides tools for the analysis and coprehension of high-throughput genomic data. racon: racon/1.4.7, racon/1.4.21, racon/1.5.0 Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. ragtag: ragtag/2.0.1-python-3.8.6 RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Tasks include: homology-based misassembly correction, homology-based assembly scaffolding and patching, and scaffold merging. RagTag also provides command line utilities for working with common genome assembly file formats. 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, raspa2/2.0.41 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. rcppgsl: rcppgsl/0.3.8-r-4.0.4 The 'RcppGSL' package provides an easy-to-use interface between 'GSL' data structures and R using concepts from 'Rcpp' which is itself a package that eases the interfaces between R and C++. 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/2.0.3 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 repeatmasker: repeatmasker/4.1.2-p1 RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. repeatscout: repeatscout/1.0.6 De Novo Repeat Finder, Price A.L., Jones N.C. and Pevzner P.A. Developed and tested with our multiple sequence version of RepeatScout ( 1.0.6 ) 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. rmats-turbo: rmats-turbo/4.1.2 rMATS turbo is the C/Cython version of rMATS (refer to http://rnaseq-mats.sourceforge.net). rmblast: rmblast/2.11.0 RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite. The primary difference between this distribution and the NCBI distribution is the addition of a new program 'rmblastn' for use with RepeatMasker and RepeatModeler. 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, ... 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 rstudio-server: rstudio-server/1.3.1093-java-11.0.2-r-3.6.2, ... This is the RStudio Server version. RStudio is a set of integrated tools designed to help you be more productive with R. The server can be started with: rserver --server-daemonize=0 --www-port 8787 --rsession-which-r=$(which R) ruby: ruby/2.6.3, ruby/2.7.1, ruby/2.7.2-mpich-3.4.2, ... 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. rush: rush/0.5.0 A cross-platform command-line tool for executing jobs in parallel rust: rust/1.37.0, rust/1.48.0, rust/1.52.1, rust/1.54.0, rust/1.65.0 Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety. sablotron: sablotron/1.0.3 Sablotron XML processor salmon: salmon/0.8.2, salmon/1.0.0, salmon/1.4.0 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/1.11, samtools/1.12, samtools/1.13, ... 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-fb, 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 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, ... Bundle of Python packages for scientific software scons: scons/3.1.1, scons/4.0.1 SCons is a software construction tool. scotch: scotch/6.0.9, scotch/6.1.0, scotch/6.1.2 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, sdl2/2.0.10, sdl2/2.0.14 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/0.9.1-python-2.7.18, ... 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, sepp/4.4.0 SATe-enabled Phylogenetic Placement - addresses the problem of phylogenetic placement of short reads into reference alignments and trees. seqan: seqan/2.4.0 SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. seqkit: seqkit/2.2.0 SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation 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 setuptools: setuptools/57.4.0-python-3.7.4, ... Setuptools is a fully-featured, actively-maintained, and stable library designed to facilitate packaging Python projects. 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. shapeit: shapeit/2.r904.glibcv2.17 SHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data. shapeit4: shapeit4/4.2.2 SHAPEIT4 is a fast and accurate method for estimation of haplotypes (aka phasing) for SNP array and high coverage sequencing data. 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, shrinkwrap/1.1.0 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 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/3.18.1 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/3.7.1, slim/4.0.1 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, snakemake/6.6.1 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/1.1.8, snappy/1.1.9 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. snptest: snptest/2.5.2 SNPTEST is a program for the analysis of single SNP association in genome-wide studies. 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. soci: soci/4.0.1, soci/4.0.3 SOCI is a database access library for C++ that makes the illusion of embedding SQL queries in the regular C++ code, staying entirely within the Standard C++. somalier: somalier/0.2.10 Extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF spack: spack/0.17.0 Spack is a package manager for supercomputers, Linux, and macOS. It makes installing scientific software easy. With Spack, you can build a package with multiple versions, configurations, platforms, and compilers, and all of these builds can coexist on the same machine. spades: spades/3.13.0, spades/3.14.0-python-3.7.4, ... Genome assembler for single-cell and isolates data sets sparsehash: sparsehash/2.0.3, sparsehash/2.0.4 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 spectra: spectra/1.0.1 Spectra stands for Sparse Eigenvalue Computation Toolkit as a Redesigned ARPACK. It is a C++ library for large scale eigenvalue problems, built on top of Eigen, an open source linear algebra library. spm: spm/12.5_r7771-matlab-2021b SPM (Statistical Parametric Mapping) refers to the construction and assessment of spatially extended statistical processes used to test hypo- theses 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. spoa: spoa/4.0.7 Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) algorithm which is used to generate consensus sequences sqlite: sqlite/3.29.0, sqlite/3.32.3, sqlite/3.33.0, sqlite/3.35.4, ... SQLite: SQL Database Engine in a C Library sra-toolkit: sra-toolkit/2.9.6-1-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 srprism: srprism/3.1.2 Single Read Paired Read Indel Substitution Minimizer 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/2.7.8a, star/2.7.9a 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. statistics-r: statistics-r/0.34 Perl interface with the R statistical program statsmodels: statsmodels/0.11.0-python-3.7.4, statsmodels/0.12.1 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/2.1.7 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 superlu: superlu/5.2.2 SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines. 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 suppa: suppa/2.3 A tool to study splicing across multiple conditions at high speed and accuracy. swash: swash/7.01-mpi 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. 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 is a collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures. tabix: tabix/0.2.6 Generic indexer for TAB-delimited genome position files taxator-tk: taxator-tk/1.3.3 A set of programs for the taxonomic analysis of nucleotide sequence data 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/8.6.11 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/6.22.03 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, ... An open-source software library for Machine Intelligence tensorflow-probability: tensorflow-probability/0.9.0-python-3.7.4 TensorFlow Probability (TFP) is a library for probabilistic reasoning and statistical analysis. tesseract: tesseract/4.1.0, tesseract/5.2.0 Tesseract is an optical character recognition engine tetgen: tetgen/1.5.0, tetgen/1.6.0 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, texlive/20210325 TeX is a typesetting language. Instead of visually formatting your text, you enter your manuscript text intertwined with TeX commands in a plain text file. You then run TeX to produce formatted output, such as a PDF file. Thus, in contrast to standard word processors, your document is a separate file that does not pretend to be a representation of the final typeset output, and so can be easily edited and manipulated. theano: theano/1.0.4-python-3.7.4, theano/1.0.4, ... Theano-PyMC is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently. theano-pymc: theano-pymc/1.1.2-python-3.8.6 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/8.6.10, tk/8.6.11 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/2.7.18, tkinter/3.7.4, tkinter/3.8.2, ... 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. toolshed: toolshed/0.4.7-python-3.8.2 brentp's common library 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, tqdm/4.56.2, tqdm/4.60.0 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, trf/4.09.1 Tandem Repeats Finder: a program to analyze DNA sequences. 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-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/2.13.0, trinity/2.13.2 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/3.2.2 Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. trnascan-se: trnascan-se/2.0.10 A program for detection of tRNA genes trust4: trust4/1.0.4-python-3.7.4, trust4/1.0.7-python-3.7.4 Tcr Receptor Utilities for Solid Tissue (TRUST) is a computational tool to analyze TCR and BCR sequences using unselected RNA sequencing data, profiled from solid tissues, including tumors. 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-3.7.4, ... Typing Extensions – Backported and Experimental Type Hints for Python ucsc: ucsc/21072020 This directory contains ucsc applications for stand-alone use. ucx: ucx/1.10.0, ucx/1.12.1 Unified Communication X An open-source production grade communication framework for data centric and high-performance applications ucx-cuda: ucx-cuda/1.12.1-cuda-10.1.243, ucx-cuda/1.12.1-cuda-11.1.1, ... Unified Communication X An open-source production grade communication framework for data centric and high-performance applications This module adds the UCX CUDA support. udunits: udunits/2.2.26, udunits/2.2.28 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. unimap: unimap/0.1 Unimap is a fork of minimap2 optimized for assembly-to-reference alignment. It integrates the minigraph chaining algorithm and can align through long INDELs (up to 100kb by default) much faster than minimap2. Unimap is a better fit for resolving segmental duplications and is recommended over minimap2 for alignment between high-quality assemblies. Unimap does not replace minimap2 for other types of alignment. It drops the support of multi-part index and short-read mapping. Its long-read alignment is different from minimap2 but is not necessarily better. Unimap is more of a specialized minimap2 at the moment. 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, unrar/6.0.2 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/2.5.0 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, util-linux/2.37 Set of Linux utilities v8: v8/3.4.0-r-3.6.2, v8/3.4.0-r-4.0.0 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 vaspkit: vaspkit/1.2.5-python-3.7.4 VASPKIT aims at providing a powerful and user-friendly interface to perform high throughput analysis of various material properties from the raw calculated data using the widely-used VASP code. The program can be conveniently run under either the interactive user interface or command line mode. vbz-compression: vbz-compression/1.0.1-test, vbz-compression/1.0.1 VBZ compression HDF5 plugin for nanopolish 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, ... 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. vg: vg/1.32.0 Variation graphs provide a succinct encoding of the sequences of many genomes. A variation graph (in particular as implemented in vg) is composed of: 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/1.9.4a51 VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. vmtouch: vmtouch/1.3.1 vmtouch is a tool for learning about and controlling the file system cache of unix and unix-like systems. 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, vtk/9.0.1, ... 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. vtune: vtune/2022.3.0 Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java. 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+/2.27.4 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, wget/1.20.3 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. whatshap: whatshap/1.4 WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly. It is especially suitable for long reads, but works also well with short reads. wine: wine/4.0.4, wine/6.15 Wine (originally an acronym for "Wine Is Not an Emulator") is a compatibility layer capable of running Windows applications on several POSIX-compliant operating systems. wine32: wine32/6.15 Wine (originally an acronym for "Wine Is Not an Emulator") is a compatibility layer capable of running Windows applications on several POSIX-compliant operating systems. 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, x11/20210518, x11/20210802 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++/3.2.3 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-libxml: xml-libxml/2.0201-perl-5.30.0, xml-libxml/2.0206 Perl binding for libxml2 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, xorg-macros/1.19.3 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, xprop/1.2.5 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. xtb: xtb/6.4.1 xtb - An extended tight-binding semi-empirical program package. 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/1.20.9, xvfb/1.20.13 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 z3: z3/4.8.10 Z3 is a theorem prover from Microsoft Research. zeromq: zeromq/4.3.2, zeromq/4.3.3 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/1.2.12 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, zstd/1.4.5, zstd/1.4.9, zstd/1.5.0 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 ----------------------------------------------------------------------------