ABySS

Description: Assembly By Short Sequences Homepage: https://www.bcgsc.ca/platform/bioinfo/software/abyss

Installed versions: - ABySS/2.0.2-gompi-2019a

</details>

AdapterRemoval

Description: AdapterRemoval searches for and removes remnant adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. Homepage: https://github.com/%/(github_account)s/adapterremoval

Installed versions: - AdapterRemoval/2.3.1-GCC-8.2.0-2.31.1 - AdapterRemoval/2.3.1-foss-2018b

</details>

ADF

Description: ADF is an accurate, parallelized, powerful computational chemistry program to understand and predict chemical structure and reactivity with density functional theory (DFT). Homepage: http://www.scm.com/ADF/

Installed versions: - ADF/2019.103+StaticMKL

</details>

AdmixTools

Description: ADMIXTOOLS is a software package that supports formal tests of whether admixture occurred, and makes it possible to infer admixture proportions and dates Homepage: https://github.com/DReichLab/AdmixTools

Installed versions: - AdmixTools/5.1-GCC-7.3.0-2.30

</details>

ADMIXTURE

Description: ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm. Homepage: http://software.genetics.ucla.edu/admixture

Installed versions: - ADMIXTURE/1.3.0

</details>

Amber

Description: Amber (originally Assisted Model Building with Energy Refinement) is software for performing molecular dynamics and structure prediction. Homepage: http://ambermd.org/amber.html

Installed versions: - Amber/18-foss-2018b-AmberTools-18-patchlevel-10-8 - Amber/18-fosscuda-2018b-AmberTools-18-patchlevel-10-8

</details>

Anaconda2

Description: 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.

Homepage: https://www.continuum.io/anaconda-overview

Installed versions: - Anaconda2/2019.03

</details>

Anaconda3

Description: 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.

Homepage: https://www.continuum.io/anaconda-overview

Installed versions: - Anaconda3/2019.03

</details>

Ancestry_HMM

Description: A hidden Markov model approach for simultaneously estimating local ancestry. Homepage: https://github.com/russcd/Ancestry_HMM

Installed versions: - Ancestry_HMM/200105-foss-2019a

</details>

angsd

Description: Program for analysing NGS data. Homepage: http://www.popgen.dk/angsd

Installed versions: - angsd/0.925-foss-2018b - angsd/0.928-GCC-7.3.0-2.30 - angsd/0.931-GCC-8.2.0-2.31.1

</details>

angsd-wrapper

Description: ANGSD-wrapper is a utility developed to aid in the analysis of next generation sequencing data Homepage: https://github.com/ANGSD-wrapper/angsd-wrapper

Installed versions: - angsd-wrapper/190321-GCC-7.3.0-2.30

</details>

ant

Description: Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications. Homepage: http://ant.apache.org/

Installed versions: - ant/1.10.5-Java-1.8

</details>

ANTLR

Description: 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. Homepage: http://www.antlr2.org/

Installed versions: - ANTLR/2.7.7-GCCcore-7.3.0

</details>

APR

Description: Apache Portable Runtime (APR) libraries. Homepage: http://apr.apache.org/

Installed versions: - APR/1.6.3-GCCcore-7.3.0 - APR/1.7.0-GCCcore-8.2.0

</details>

APR-util

Description: Apache Portable Runtime (APR) util libraries. Homepage: http://apr.apache.org/

Installed versions: - APR-util/1.6.1-GCCcore-7.3.0 - APR-util/1.6.1-GCCcore-8.2.0

</details>

ARKS

Description: Scaffolding genome sequence assemblies using 10X Genomics GemCode/Chromium data Homepage: https://github.com/bcgsc/arcs

Installed versions: - ARKS/1.0.4-gompi-2019a

</details>

Arm-PerfReports

Description: Single page HTML profiler for parallel programs. Homepage: https://developer.arm.com/products/software-development-tools/hpc

Installed versions: - Arm-PerfReports/19.1

</details>

Armadillo

Description: 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. Homepage: https://arma.sourceforge.net/

Installed versions: - Armadillo/9.700.2-foss-2019a

</details>

arpack-ng

Description: ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. Homepage: https://github.com/opencollab/arpack-ng

Installed versions: - arpack-ng/3.7.0-foss-2019a

</details>

ASE

Description: ASE is a python package providing an open source Atomic Simulation Environment in the Python scripting language. Homepage: https://wiki.fysik.dtu.dk/ase

Installed versions: - ASE/3.17.0-foss-2018b-Python-3.6.6 - ASE/3.17.0-intel-2018b-Python-3.6.6 - ASE/3.18.0-foss-2019a-Python-3.7.2 - ASE/3.18.0-intel-2019a-Python-3.7.2

</details>

AUGUSTUS

Description: AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences Homepage: http://bioinf.uni-greifswald.de/augustus/

Installed versions: - AUGUSTUS/3.3.2-intel-2018b-Python-2.7.15

</details>

Autoconf

Description: 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.

Homepage: http://www.gnu.org/software/autoconf/

Installed versions: - Autoconf/2.69-GCCcore-6.4.0 - Autoconf/2.69-GCCcore-7.3.0 - Autoconf/2.69-GCCcore-8.2.0 - Autoconf/2.69-GCCcore-8.3.0

</details>

Automake

Description: Automake: GNU Standards-compliant Makefile generator Homepage: http://www.gnu.org/software/automake/automake.html

Installed versions: - Automake/1.15.1-GCCcore-6.4.0 - Automake/1.15.1-GCCcore-7.3.0 - Automake/1.15.1-GCCcore-8.2.0 - Automake/1.16.1-GCCcore-7.3.0 - Automake/1.16.1-GCCcore-8.2.0 - Automake/1.16.1-GCCcore-8.3.0

</details>

Autotools

Description: This bundle collect the standard GNU build tools: Autoconf, Automake and libtool

Homepage: http://autotools.io

Installed versions: - Autotools/20170619-GCCcore-6.4.0 - Autotools/20170619-GCCcore-7.3.0 - Autotools/20170619-GCCcore-8.2.0 - Autotools/20180311-GCCcore-7.3.0 - Autotools/20180311-GCCcore-8.2.0 - Autotools/20180311-GCCcore-8.3.0

</details>

BAMM

Description: 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. Homepage: http://bamm-project.org/

Installed versions: - BAMM/2.5.0-foss-2018b

</details>

BamTools

Description: BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files. Homepage: https://github.com/pezmaster31/bamtools

Installed versions: - BamTools/2.5.1-GCC-8.2.0-2.31.1 - BamTools/2.5.1-foss-2018b - BamTools/2.5.1-iccifort-2019.1.144-GCC-8.2.0-2.31.1 - BamTools/2.5.1-intel-2018b

</details>

BayeScan

Description: BayeScan aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. Homepage: http://cmpg.unibe.ch/software/BayeScan/

Installed versions: - BayeScan/2.1-foss-2018b - BayeScan/2.1-intel-2018b

</details>

BayeScEnv

Description: BayeScEnv is a Fst-based, genome-scan method that uses environmental variables to detect local adaptation. Homepage: https://github.com/devillemereuil/bayescenv

Installed versions: - BayeScEnv/1.1-foss-2018b

</details>

Bazel

Description: Bazel is a build tool that builds code quickly and reliably. It is used to build the majority of Google's software. Homepage: https://bazel.io/

Installed versions: - Bazel/0.18.0-GCCcore-7.3.0 - Bazel/0.20.0-GCCcore-7.3.0 - Bazel/0.29.1-GCCcore-8.3.0

</details>

BBMap

Description: BBMap short read aligner, and other bioinformatic tools. Homepage: https://sourceforge.net/projects/bbmap/

Installed versions: - BBMap/38.50b-GCC-8.2.0-2.31.1

</details>

BCFtools

Description: Samtools is a suite of programs for interacting with high-throughput sequencing data. BCFtools Homepage: http://www.htslib.org/

Installed versions: - BCFtools/1.9-foss-2018b - BCFtools/1.9-intel-2018b

</details>

bcolz

Description: bcolz provides columnar, chunked data containers that can be compressed either in-memory and on-disk. Column storage allows for efficiently querying tables, as well as for cheap column addition and removal. It is based on NumPy, and uses it as the standard data container to communicate with bcolz objects, but it also comes with support for import/export facilities to/from HDF5/PyTables tables and pandas dataframes. Homepage: http://bcolz.blosc.org/en/latest/

Installed versions: - bcolz/1.2.1-foss-2019a-Python-3.7.2

</details>

Beagle

Description: Beagle is a software package for phasing genotypes and for imputing ungenotyped markers Homepage: http://faculty.washington.edu/browning/beagle/beagle.html

Installed versions: - Beagle/4.1-Java-1.8 - Beagle/5.1-Java-11

</details>

beagle-lib

Description: beagle-lib is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. Homepage: https://github.com/beagle-dev/beagle-lib

Installed versions: - beagle-lib/3.0.2-foss-2018b - beagle-lib/3.1.2-GCC-8.2.0-2.31.1

</details>

Beast

Description: 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. Homepage: http://beast2.org/

Installed versions: - Beast/2.5.2-GCC-8.2.0-2.31.1

</details>

BEDTools

Description: 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. Homepage: https://github.com/arq5x/bedtools2

Installed versions: - BEDTools/2.27.1-foss-2018b - BEDTools/2.27.1-intel-2018b - BEDTools/2.28.0-GCC-8.2.0-2.31.1 - BEDTools/2.28.0-iccifort-2019.1.144-GCC-8.2.0-2.31.1

</details>

BEEF

Description: BEEF-vdW functionals and Bayesian error estimates to Fortran- or C-based DFT codes. Homepage: https://confluence.slac.stanford.edu/display/SUNCAT/BEEF+Functional+Software

Installed versions: - BEEF/0.1.1-intel-2019a

</details>

binutils

Description: binutils: GNU binary utilities Homepage: http://directory.fsf.org/project/binutils/

Installed versions: - binutils/2.28 - binutils/2.28-GCCcore-6.4.0 - binutils/2.30 - binutils/2.30-GCCcore-7.3.0 - binutils/2.31.1 - binutils/2.31.1-GCCcore-8.2.0 - binutils/2.32 - binutils/2.32-GCCcore-8.3.0

</details>

BioPerl

Description: 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. Homepage: http://www.bioperl.org/

Installed versions: - BioPerl/1.7.2-GCCcore-8.3.0 - BioPerl/1.7.2-foss-2018b-Perl-5.28.0

</details>

Biopython

Description: 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. Homepage: http://www.biopython.org

Installed versions: - Biopython/1.73-foss-2019a - Biopython/1.73-intel-2019a

</details>

Bison

Description: 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.

Homepage: http://www.gnu.org/software/bison

Installed versions: - Bison/3.0.4 - Bison/3.0.4-GCCcore-6.4.0 - Bison/3.0.4-GCCcore-7.3.0 - Bison/3.0.5 - Bison/3.0.5-GCCcore-6.4.0 - Bison/3.0.5-GCCcore-7.3.0 - Bison/3.0.5-GCCcore-8.2.0 - Bison/3.3.2 - Bison/3.3.2-GCCcore-8.3.0

</details>

BLAST+

Description: 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. Homepage: http://blast.ncbi.nlm.nih.gov/

Installed versions: - BLAST+/2.8.1-foss-2018b - BLAST+/2.8.1-intel-2018b - BLAST+/2.9.0-gompi-2019a - BLAST+/2.9.0-gompi-2019b - BLAST+/2.9.0-iimpi-2019a

</details>

BLAT

Description: BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more. Homepage: https://genome.ucsc.edu/FAQ/FAQblat.html

Installed versions: - BLAT/3.5-GCC-8.2.0-2.31.1

</details>

BlobTools

Description: A modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets. Homepage: https://blobtools.readme.io/docs

Installed versions: - BlobTools/20180528-foss-2018b-Python-2.7.15

</details>

Blosc

Description: Blosc, an extremely fast, multi-threaded, meta-compressor library Homepage: http://www.blosc.org/

Installed versions: - Blosc/1.17.0-GCCcore-8.2.0

</details>

bokeh

Description: Statistical and novel interactive HTML plots for Python Homepage: http://github.com/bokeh/bokeh

Installed versions: - bokeh/1.3.4-foss-2019a-Python-3.7.2

</details>

Boost

Description: Boost provides free peer-reviewed portable C++ source libraries. Homepage: https://www.boost.org/

Installed versions: - Boost/1.65.1-intel-2018b - Boost/1.67.0-foss-2018b - Boost/1.67.0-fosscuda-2018b - Boost/1.67.0-intel-2018b - Boost/1.68.0-foss-2018b-Python-2.7.15 - Boost/1.68.0-foss-2018b-Python-3.6.6 - Boost/1.68.0-intel-2018b-Python-2.7.15 - Boost/1.68.0-intel-2018b-Python-3.6.6 - Boost/1.70.0-gompi-2019a - Boost/1.70.0-iimpi-2019a - Boost/1.71.0-gompi-2019b - Boost/1.71.0-iimpi-2019b

</details>

Boost.Python

Description: Boost.Python is a C++ library which enables seamless interoperability between C++ and the Python programming language. Homepage: http://boostorg.github.io/python

Installed versions: - Boost.Python/1.67.0-foss-2018b-Python-2.7.15 - Boost.Python/1.67.0-foss-2018b-Python-3.6.6 - Boost.Python/1.67.0-fosscuda-2018b-Python-2.7.15 - Boost.Python/1.67.0-intel-2018b-Python-2.7.15 - Boost.Python/1.67.0-intel-2018b-Python-3.6.6 - Boost.Python/1.70.0-gompi-2019a - Boost.Python/1.70.0-iimpi-2019a

</details>

Bowtie

Description: Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome. Homepage: http://bowtie-bio.sourceforge.net/index.shtml

Installed versions: - Bowtie/1.2.2-foss-2018b

</details>

Bowtie2

Description: 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. Homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml

Installed versions: - Bowtie2/2.3.4.2-foss-2018b - Bowtie2/2.3.4.2-intel-2018b - Bowtie2/2.3.5.1-GCC-8.2.0-2.31.1 - Bowtie2/2.3.5.1-iccifort-2019.1.144-GCC-8.2.0-2.31.1

</details>

BreakDancer

Description: BreakDancer is a Perl/C++ package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads Homepage: http://gmt.genome.wustl.edu/packages/breakdancer

Installed versions: - BreakDancer/1.4.5-intel-2018b

</details>

BSMAP

Description: BSMAP is a short reads mapping software for bisulfite sequencing reads. Homepage: https://code.google.com/p/bsmap/

Installed versions: - BSMAP/2.90-foss-2018b

</details>

BUSCO

Description: BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs Homepage: http://busco.ezlab.org/

Installed versions: - BUSCO/3.0.2-intel-2018b-Python-2.7.15

</details>

BWA

Description: Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. Homepage: http://bio-bwa.sourceforge.net/

Installed versions: - BWA/0.7.17-GCC-8.2.0-2.31.1 - BWA/0.7.17-foss-2018b - BWA/0.7.17-intel-2018b

</details>

bzip2

Description: 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.

Homepage: https://sourceware.org/bzip2

Installed versions: - bzip2/1.0.6-GCCcore-7.3.0 - bzip2/1.0.6-GCCcore-8.2.0 - bzip2/1.0.8-GCCcore-8.3.0

</details>

cairo

Description: 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 Homepage: https://cairographics.org

Installed versions: - cairo/1.14.12-GCCcore-7.3.0 - cairo/1.16.0-GCCcore-8.2.0 - cairo/1.16.0-GCCcore-8.3.0

</details>

canu

Description: Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing Homepage: http://canu.readthedocs.io

Installed versions: - canu/1.8-GCCcore-8.2.0-Perl-5.28.1 - canu/1.8-foss-2018b-Perl-5.28.0

</details>

CD-HIT

Description: CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences. Homepage: http://weizhong-lab.ucsd.edu/cd-hit/

Installed versions: - CD-HIT/4.8.1-foss-2018b - CD-HIT/4.8.1-foss-2019a - CD-HIT/4.8.1-intel-2018b

</details>

CDO

Description: CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data. Homepage: https://code.zmaw.de/projects/cdo

Installed versions: - CDO/1.9.5-intel-2018b - CDO/1.9.8-intel-2019b

</details>

CFITSIO

Description: CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format. Homepage: https://heasarc.gsfc.nasa.gov/fitsio/

Installed versions: - CFITSIO/3.47-GCCcore-8.2.0

</details>

cftime

Description: Time-handling functionality from netcdf4-python Homepage: https://github.com/Unidata/cftime

Installed versions: - cftime/1.0.1-foss-2018b-Python-3.6.6 - cftime/1.0.1-intel-2018b-Python-3.6.6

</details>

CGAL

Description: 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. Homepage: http://www.cgal.org/

Installed versions: - CGAL/4.11.1-foss-2018b-Python-2.7.15 - CGAL/4.11.1-foss-2018b-Python-3.6.6

</details>

CheckM

Description: CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. Homepage: https://github.com/Ecogenomics/CheckM

Installed versions: - CheckM/1.0.13-foss-2018b-Python-2.7.15 - CheckM/1.0.18-foss-2019a-Python-2.7.15

</details>

Circlator

Description: A tool to circularize genome assemblies. Homepage: https://sanger-pathogens.github.io/circlator

Installed versions: - Circlator/1.5.5-foss-2018b-Python-3.6.6

</details>

Clang

Description: C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC. Homepage: https://clang.llvm.org/

Installed versions: - Clang/9.0.1-GCCcore-8.3.0

</details>

CMake

Description: CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.

Homepage: http://www.cmake.org

Installed versions: - CMake/3.9.1-GCCcore-7.3.0 - CMake/3.9.4-GCCcore-7.3.0 - CMake/3.11.4-GCCcore-7.3.0 - CMake/3.12.1 - CMake/3.12.1-GCCcore-7.3.0 - CMake/3.13.3-GCCcore-8.2.0 - CMake/3.15.3-GCCcore-8.3.0

</details>

CP2K

Description: CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials. Homepage: http://www.cp2k.org/

Installed versions: - CP2K/6.1-foss-2019a - CP2K/6.1-intel-2018a

</details>

CUDA

Description: 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. Homepage: https://developer.nvidia.com/cuda-toolkit

Installed versions: - CUDA/9.2.88-GCC-7.3.0-2.30 - CUDA/10.0.130 - CUDA/10.1.105 - CUDA/10.1.105-GCC-8.2.0-2.31.1 - CUDA/10.1.105-iccifort-2019.1.144-GCC-8.2.0-2.31.1 - CUDA/10.1.243 - CUDA/10.1.243-GCC-8.3.0 - CUDA/10.1.243-iccifort-2019.5.281

</details>

cuDNN

Description: The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks. Homepage: https://developer.nvidia.com/cudnn

Installed versions: - cuDNN/7.1.4.18-fosscuda-2018b - cuDNN/7.4.2.24-CUDA-10.0.130 - cuDNN/7.6.4.38 - cuDNN/7.6.4.38-CUDA-10.1.105 - cuDNN/7.6.4.38-CUDA-10.1.243 - cuDNN/7.6.4.38-gcccuda-2019a - cuDNN/7.6.4.38-gcccuda-2019b

</details>

Description: Transcript assembly, differential expression, and differential regulation for RNA-Seq Homepage: http://cole-trapnell-lab.github.io/cufflinks/

Installed versions: - Cufflinks/20190706-gompi-2019a

</details>

cURL

Description: 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.

Homepage: https://curl.haxx.se

Installed versions: - cURL/7.60.0-GCCcore-7.3.0 - cURL/7.63.0-GCCcore-8.2.0 - cURL/7.66.0-GCCcore-8.3.0

</details>

cutadapt

Description: Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Homepage: http://opensource.scilifelab.se/projects/cutadapt/

Installed versions: - cutadapt/1.18-foss-2018b-Python-3.6.6

</details>

Cython

Description: Cython is an optimising static compiler for both the Python programming language and the extended Cython programming language (based on Pyrex).

Homepage: https://cython.org/

Installed versions: - Cython/0.27.3-GCCcore-8.2.0-Python-2.7.15

</details>

dadi

Description: ∂a∂i implements methods for demographic history and selection inference from genetic data, based on diffusion approximations to the allele frequency spectrum. Homepage: https://bitbucket.org/gutenkunstlab/dadi

Installed versions: - dadi/2.0.1-intel-2019a-Python-3.7.2

</details>

dask

Description: Dask natively scales Python. Dask provides advanced parallelism for analytics, enabling performance at scale for the tools you love. Homepage: https://dask.org/

Installed versions: - dask/2.3.0-foss-2019a-Python-3.7.2

</details>

DBus

Description: 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.

Homepage: http://dbus.freedesktop.org/

Installed versions: - DBus/1.13.6-GCCcore-7.3.0 - DBus/1.13.8-GCCcore-8.2.0 - DBus/1.13.12-GCCcore-8.3.0

</details>

deepTools

Description: 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. Homepage: https://deeptools.readthedocs.io/

Installed versions: - deepTools/3.3.0-intel-2019a-Python-3.7.2

</details>

DendroPy

Description: A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters. Homepage: https://pypi.python.org/pypi/DendroPy/

Installed versions: - DendroPy/4.4.0-GCCcore-8.2.0

</details>

DFT-D3

Description: DFT-D3 implements a dispersion correction for density functionals, Hartree-Fock and semi-empirical quantum chemical methods. Homepage: http://www.thch.uni-bonn.de/tc/index.php?section=downloads&subsection=DFT-D3&lang=english

Installed versions: - DFT-D3/3.2.0-intel-2019a

</details>

DIAMOND

Description: DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data. Homepage: https://github.com/bbuchfink/diamond

Installed versions: - DIAMOND/0.9.24-iccifort-2019.1.144-GCC-8.2.0-2.31.1

</details>

double-conversion

Description: Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles. Homepage: https://github.com/google/double-conversion

Installed versions: - double-conversion/3.1.4-GCCcore-8.3.0

</details>

Doxygen

Description: 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.

Homepage: https://www.doxygen.org

Installed versions: - Doxygen/1.8.13-GCCcore-7.3.0 - Doxygen/1.8.14-GCCcore-7.3.0 - Doxygen/1.8.15-GCCcore-8.2.0 - Doxygen/1.8.16-GCCcore-8.3.0

</details>

EasyBuild

Description: EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way. Homepage: https://easybuilders.github.io/easybuild

Installed versions: - EasyBuild/3.9.2 - EasyBuild/3.9.3 - EasyBuild/3.9.4 - EasyBuild/4.0.0 - EasyBuild/4.0.1 - EasyBuild/4.1.0 - EasyBuild/4.1.1

</details>

ecCodes

Description: 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). Homepage: https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home

Installed versions: - ecCodes/2.9.2-intel-2018b - ecCodes/2.15.0-iimpi-2019b

</details>

ecoPCR

Description: A tool for estimating DNA Barcode primers quality. Homepage: https://git.metabarcoding.org/obitools/ecopcr/wikis/home

Installed versions: - ecoPCR/1.0.1-foss-2019a-Python-2.7.15

</details>

ecoPrimers

Description: ecoPrimers is a software that finds primers from a set of sequences Homepage: https://git.metabarcoding.org/obitools/ecoprimers/wikis/home

Installed versions: - ecoPrimers/0.5-GCC-7.3.0-2.30

</details>

Eigen

Description: Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms. Homepage: http://eigen.tuxfamily.org/index.php?title=Main_Page

Installed versions: - Eigen/3.3.7

</details>

EIGENSOFT

Description: 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. Homepage: http://www.hsph.harvard.edu/alkes-price/software/

Installed versions: - EIGENSOFT/7.2.1-foss-2018b - EIGENSOFT/7.2.1-foss-2019a - EIGENSOFT/7.2.1-intel-2018b - EIGENSOFT/7.2.1-intel-2019a

</details>

ELPA

Description: Eigenvalue SoLvers for Petaflop-Applications . Homepage: http://elpa.rzg.mpg.de

Installed versions: - ELPA/2016.11.001.pre-intel-2018b - ELPA/2017.11.001-foss-2019a - ELPA/2017.11.001-intel-2018a - ELPA/2018.11.001-intel-2019a

</details>

Emacs

Description: 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. Homepage: http://www.gnu.org/software/emacs/

Installed versions: - Emacs/25.3-GCCcore-7.3.0

</details>

EMBOSS

Description: 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. Homepage: http://emboss.sourceforge.net/

Installed versions: - EMBOSS/6.6.0-foss-2018b - EMBOSS/6.6.0-intel-2018b

</details>

ExaML

Description: Exascale Maximum Likelihood (ExaML) code for phylogenetic inference using MPI. Homepage: https://github.com/amkozlov/ExaML

Installed versions: - ExaML/3.0.21-foss-2019a

</details>

Exonerate

Description: Exonerate is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics. Homepage: https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate

Installed versions: - Exonerate/2.4.0-GCC-8.2.0-2.31.1

</details>

expat

Description: 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)

Homepage: https://libexpat.github.io

Installed versions: - expat/2.2.5-GCCcore-7.3.0 - expat/2.2.6-GCCcore-8.2.0 - expat/2.2.7-GCCcore-8.3.0

</details>

extractPIRs

Description: Tool to extract the PIRs from BAM files that relies on the samtools API for efficiency Homepage: https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html

Installed versions: - extractPIRs/1.r68.x86_64

</details>

FastME

Description: FastME: a comprehensive, accurate and fast distance-based phylogeny inference program. Homepage: http://www.atgc-montpellier.fr/fastme/

Installed versions: - FastME/2.1.6.1-intel-2018b

</details>

fastNGSadmix

Description: fastNGSadmix is a program for infering admixture proportions and doing PCA with a single NGS sample Homepage: https://github.com/e-jorsboe/fastNGSadmix

Installed versions: - fastNGSadmix/190518-foss-2019a-R-3.6.0

</details>

FastQC

Description: 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. Homepage: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Installed versions: - FastQC/0.11.8-Java-1.8

</details>

fastsimcoal2

Description: Fast sequential markov coalescent simulation of genomic data under complex evolutionary models Homepage: http://cmpg.unibe.ch/software/fastsimcoal2/

Installed versions: - fastsimcoal2/6.0.3-linux64

</details>

FastTree

Description: 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. Homepage: http://www.microbesonline.org/fasttree/

Installed versions: - FastTree/2.1.10-foss-2018b - FastTree/2.1.10-intel-2018b - FastTree/2.1.11-GCCcore-8.2.0

</details>

FASTX-Toolkit

Description: The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. Homepage: http://hannonlab.cshl.edu/fastx_toolkit/

Installed versions: - FASTX-Toolkit/0.0.14-intel-2018b

</details>

FFC

Description: The FEniCS Form Compiler (FFC) is a compiler for finite element variational forms. Homepage: https://bitbucket.org/fenics-project/ffc

Installed versions: - FFC/2018.1.0-foss-2018b-Python-3.6.6

</details>

FFTW

Description: FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data. Homepage: http://www.fftw.org

Installed versions: - FFTW/3.3.7-intel-2018a - FFTW/3.3.8-gompi-2018b - FFTW/3.3.8-gompi-2019a - FFTW/3.3.8-gompi-2019b - FFTW/3.3.8-gompic-2018b - FFTW/3.3.8-intel-2018b - FFTW/3.3.8-intel-2019a - FFTW/3.3.8-intel-2019b

</details>

FIAT

Description: 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. Homepage: https://bitbucket.org/fenics-project/fiat

Installed versions: - FIAT/2018.1.0-foss-2018b-Python-3.6.6

</details>

file

Description: 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. Homepage: http://www.darwinsys.com/file/

Installed versions: - file/5.35-GCCcore-7.3.0

</details>

fineRADstructure

Description: A package for population structure inference from RAD-seq data Homepage: http://cichlid.gurdon.cam.ac.uk/fineRADstructure.html

Installed versions: - fineRADstructure/0.3.2r109-intel-2018b

</details>

fineSTRUCTURE

Description: fineSTRUCTURE is a fast and powerful algorithm for identifying population structure using dense sequencing data. Homepage: https://people.maths.bris.ac.uk/~madjl/finestructure/finestructure_info.html

Installed versions: - fineSTRUCTURE/2.1.3-GCC-7.3.0-2.30

</details>

flex

Description: 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.

Homepage: http://flex.sourceforge.net/

Installed versions: - flex/2.6.3 - flex/2.6.4 - flex/2.6.4-GCCcore-6.4.0 - flex/2.6.4-GCCcore-7.3.0 - flex/2.6.4-GCCcore-8.2.0 - flex/2.6.4-GCCcore-8.3.0

</details>

FLUENT

Description: ANSYS FLUENT software contains the broad physical modeling capabilities needed to model flow, turbulence, heat transfer, and reactions for industrial applications ranging from air flow over an aircraft wing to combustion in a furnace, from bubble columns to oil platforms, from blood flow to semiconductor manufacturing, and from clean room design to wastewater treatment plants. Homepage: http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+Fluent

Installed versions: - FLUENT/19.4

</details>

fontconfig

Description: Fontconfig is a library designed to provide system-wide font configuration, customization and application access.

Homepage: https://www.freedesktop.org/wiki/Software/fontconfig/

Installed versions: - fontconfig/2.13.0-GCCcore-7.3.0 - fontconfig/2.13.1-GCCcore-8.2.0 - fontconfig/2.13.1-GCCcore-8.3.0

</details>

foss

Description: GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK. Homepage: https://easybuild.readthedocs.io/en/master/Common-toolchains.html#foss-toolchain

Installed versions: - foss/2018b - foss/2019a - foss/2019b

</details>

fosscuda

Description: GCC based compiler toolchain with CUDA support, and including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK. Homepage: (none)

Installed versions: - fosscuda/2018b

</details>

freebayes

Description: A haplotype-based variant detector. Homepage: https://github.com/ekg/freebayes

Installed versions: - freebayes/200109-foss-2019a-Python-3.7.2

</details>

freeglut

Description: freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library. Homepage: http://freeglut.sourceforge.net/

Installed versions: - freeglut/3.0.0-GCCcore-8.2.0 - freeglut/3.0.0-foss-2018b

</details>

FreeSurfer

Description: 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. Homepage: https://surfer.nmr.mgh.harvard.edu/

Installed versions: - FreeSurfer/6.0.1-centos6_x86_64

</details>

freetype

Description: 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.

Homepage: http://freetype.org

Installed versions: - freetype/2.9.1-GCCcore-7.3.0 - freetype/2.9.1-GCCcore-8.2.0 - freetype/2.10.1-GCCcore-8.3.0

</details>

FriBidi

Description: The Free Implementation of the Unicode Bidirectional Algorithm.

Homepage: https://github.com/fribidi/fribidi

Installed versions: - FriBidi/1.0.5-GCCcore-7.3.0 - FriBidi/1.0.5-GCCcore-8.2.0

</details>

FSL

Description: FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. Homepage: http://www.fmrib.ox.ac.uk/fsl/

Installed versions: - FSL/5.0.11-foss-2018b - FSL/5.0.11-foss-2018b-Python-3.6.6 - FSL/6.0.1-foss-2019a-Python-3.7.2

</details>

GATK

Description: 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. Homepage: https://www.broadinstitute.org/gatk/

Installed versions: - GATK/4.1.0.0-foss-2018b-Python-3.6.6 - GATK/4.1.0.0-intel-2018b-Python-3.6.6 - GATK/4.1.2.0-GCCcore-8.2.0-Java-1.8 - GATK/4.1.4.0-GCCcore-8.3.0-Java-1.8

</details>

Gaussian

Description: The Gaussian series of electronic structure programs provides a wide-ranging suite of the most advanced modeling capabilities available. You can use it to investigate the real-world chemical problems that interest you, in all of their complexity, even on modest computer hardware. Homepage: http://gaussian.com

Installed versions: - Gaussian/g16_B.01 - Gaussian/g16_C.01

</details>

gc

Description: The Boehm-Demers-Weiser conservative garbage collector can be used as a garbage collecting replacement for C malloc or C++ new.

Homepage: http://hboehm.info/gc/

Installed versions: - gc/7.6.0-GCCcore-6.4.0 - gc/7.6.4-GCCcore-7.3.0 - gc/7.6.10-GCCcore-8.2.0

</details>

GCC

Description: 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,...). Homepage: http://gcc.gnu.org/

Installed versions: - GCC/7.3.0-2.30 - GCC/8.2.0-2.31.1 - GCC/8.3.0

</details>

GCCcore

Description: 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,...). Homepage: http://gcc.gnu.org/

Installed versions: - GCCcore/6.4.0 - GCCcore/7.3.0 - GCCcore/8.2.0 - GCCcore/8.3.0

</details>

gcccuda

Description: GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit. Homepage: (none)

Installed versions: - gcccuda/2018b - gcccuda/2019a - gcccuda/2019b

</details>

GDAL

Description: 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. Homepage: https://www.gdal.org

Installed versions: - GDAL/2.2.3-foss-2018b-Python-3.6.6 - GDAL/2.2.3-intel-2018b-Python-3.6.6 - GDAL/2.4.0-foss-2019a-Python-3.7.2 - GDAL/3.0.0-foss-2019a-Python-3.7.2 - GDAL/3.0.0-intel-2019a-Python-3.7.2 - GDAL/3.0.1-foss-2019a-Python-3.7.2 - GDAL/3.0.2-intel-2019b-Python-3.7.4

</details>

GEOS

Description: GEOS (Geometry Engine Homepage: https://trac.osgeo.org/geos

Installed versions: - GEOS/3.6.2-foss-2018b-Python-3.6.6 - GEOS/3.6.2-intel-2018b-Python-3.6.6 - GEOS/3.7.2-foss-2019a-Python-3.7.2 - GEOS/3.7.2-intel-2019a-Python-3.7.2 - GEOS/3.8.0-iccifort-2019.5.281-Python-3.7.4

</details>

GetOrganelle

Description: The GetOrganelle toolkit assemblies organelle genome from genomic skimming data Homepage: https://github.com/Kinggerm/GetOrganelle

Installed versions: - GetOrganelle/1.6.2-foss-2019a-Python-3.7.2

</details>

gettext

Description: GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation Homepage: https://www.gnu.org/software/gettext/

Installed versions: - gettext/0.19.8.1 - gettext/0.19.8.1-GCCcore-7.3.0 - gettext/0.19.8.1-GCCcore-8.2.0 - gettext/0.20.1-GCCcore-8.3.0

</details>

Ghostscript

Description: 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. Homepage: https://ghostscript.com

Installed versions: - Ghostscript/9.27-GCCcore-8.2.0 - Ghostscript/9.50-GCCcore-8.3.0

</details>

git

Description: 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. Homepage: https://git-scm.com/

Installed versions: - git/2.18.0-GCCcore-7.3.0 - git/2.21.0-GCCcore-8.2.0 - git/2.23.0-GCCcore-8.3.0 - git/2.23.0-GCCcore-8.3.0-nodocs

</details>

GL2PS

Description: GL2PS: an OpenGL to PostScript printing library Homepage: http://www.geuz.org/gl2ps/

Installed versions: - GL2PS/1.4.0-GCCcore-8.2.0

</details>

GLib

Description: GLib is one of the base libraries of the GTK+ project Homepage: https://www.gtk.org/

Installed versions: - GLib/2.54.3-GCCcore-7.3.0 - GLib/2.60.1-GCCcore-8.2.0 - GLib/2.62.0-GCCcore-8.3.0

</details>

GLibmm

Description: C++ bindings for Glib Homepage: http://www.gtk.org/

Installed versions: - GLibmm/2.49.7-GCCcore-8.2.0

</details>

GLM

Description: OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics software based on the OpenGL Shading Language (GLSL) specifications. Homepage: https://github.com/g-truc/glm

Installed versions: - GLM/0.9.9.0-GCCcore-7.3.0 - GLM/0.9.9.4-GCCcore-8.2.0

</details>

GMAP-GSNAP

Description: GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences GSNAP: Genomic Short-read Nucleotide Alignment Program Homepage: http://research-pub.gene.com/gmap/

Installed versions: - GMAP-GSNAP/2019-03-15-foss-2018b

</details>

GMP

Description: GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers.

Homepage: https://gmplib.org/

Installed versions: - GMP/6.1.2-GCCcore-6.4.0 - GMP/6.1.2-GCCcore-7.3.0 - GMP/6.1.2-GCCcore-8.2.0 - GMP/6.1.2-GCCcore-8.3.0

</details>

gmsh

Description: Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor. Homepage: http://geuz.org/gmsh

Installed versions: - gmsh/4.2.2-foss-2018b-Python-3.6.6

</details>

gnuplot

Description: Portable interactive, function plotting utility Homepage: http://gnuplot.sourceforge.net/

Installed versions: - gnuplot/5.2.5-foss-2018b - gnuplot/5.2.6-GCCcore-8.2.0

</details>

GObject-Introspection

Description: GObject introspection is a middleware layer between C libraries (using GObject) and language bindings. The C library can be scanned at compile time and generate a metadata file, in addition to the actual native C library. Then at runtime, language bindings can read this metadata and automatically provide bindings to call into the C library. Homepage: https://wiki.gnome.org/GObjectIntrospection/

Installed versions: - GObject-Introspection/1.54.1-foss-2018b-Python-2.7.15 - GObject-Introspection/1.60.1-GCCcore-8.2.0-Python-3.7.2

</details>

gompi

Description: GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support. Homepage: (none)

Installed versions: - gompi/2018b - gompi/2019a - gompi/2019b

</details>

gompic

Description: GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, including OpenMPI for MPI support with CUDA features enabled. Homepage: (none)

Installed versions: - gompic/2018b

</details>

gperf

Description: GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single string comparison only.

Homepage: https://www.gnu.org/software/gperf/

Installed versions: - gperf/3.1-GCCcore-7.3.0 - gperf/3.1-GCCcore-8.2.0 - gperf/3.1-GCCcore-8.3.0

</details>

GROMACS

Description: 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 CPU only build, containing both MPI and threadMPI builds.

Homepage: http://www.gromacs.org

Installed versions: - GROMACS/2018.1-foss-2018b - GROMACS/2018.4-fosscuda-2018b-PLUMED-2.5.0 - GROMACS/2019-foss-2018b - GROMACS/2019.3-foss-2019a - GROMACS/2019.4-foss-2019b

</details>

GSL

Description: 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. Homepage: https://www.gnu.org/software/gsl/

Installed versions: - GSL/2.4-GCCcore-6.4.0 - GSL/2.5-GCC-7.3.0-2.30 - GSL/2.5-GCC-8.2.0-2.31.1 - GSL/2.5-iccifort-2018.3.222-GCC-7.3.0-2.30 - GSL/2.5-iccifort-2019.1.144-GCC-8.2.0-2.31.1 - GSL/2.6-GCC-8.3.0 - GSL/2.6-iccifort-2019.5.281

</details>

gtest

Description: Google's framework for writing C++ tests on a variety of platforms Homepage: https://github.com/google/googletest

Installed versions: - gtest/1.8.1-GCCcore-8.2.0

</details>

Guile

Description: 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. Homepage: https://www.gnu.org/software/guile/

Installed versions: - Guile/1.8.8-GCCcore-6.4.0 - Guile/1.8.8-GCCcore-7.3.0 - Guile/1.8.8-GCCcore-8.2.0

</details>

gzip

Description: gzip (GNU zip) is a popular data compression program as a replacement for compress Homepage: http://www.gnu.org/software/gzip/

Installed versions: - gzip/1.10-GCCcore-8.2.0

</details>

h5py

Description: 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. Homepage: http://www.h5py.org/

Installed versions: - h5py/2.8.0-foss-2018b-Python-3.6.6 - h5py/2.8.0-fosscuda-2018b-Python-3.6.6 - h5py/2.8.0-intel-2018b-Python-3.6.6 - h5py/2.9.0-foss-2019a - h5py/2.9.0-intel-2019a - h5py/2.10.0-foss-2019b-Python-3.7.4 - h5py/2.10.0-intel-2019b-Python-3.7.4

</details>

HarfBuzz

Description: HarfBuzz is an OpenType text shaping engine. Homepage: http://www.freedesktop.org/wiki/Software/HarfBuzz

Installed versions: - HarfBuzz/2.2.0-foss-2018b - HarfBuzz/2.4.0-GCCcore-8.2.0

</details>

HDF5

Description: 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. Homepage: https://portal.hdfgroup.org/display/support

Installed versions: - HDF5/1.10.1-intel-2018b - HDF5/1.10.2-foss-2018b - HDF5/1.10.2-fosscuda-2018b - HDF5/1.10.2-intel-2018b - HDF5/1.10.5-gompi-2019a - HDF5/1.10.5-gompi-2019b - HDF5/1.10.5-iimpi-2019a - HDF5/1.10.5-iimpi-2019b

</details>

help2man

Description: help2man produces simple manual pages from the '--help' and '--version' output of other commands. Homepage: https://www.gnu.org/software/help2man/

Installed versions: - help2man/1.47.4 - help2man/1.47.4-GCCcore-6.4.0 - help2man/1.47.4-GCCcore-7.3.0 - help2man/1.47.7-GCCcore-8.2.0 - help2man/1.47.8-GCCcore-8.3.0

</details>

HipSTR

Description: Haplotype inference and phasing for Short Tandem Repeats Homepage: https://github.com/tfwillems/HipSTR

Installed versions: - HipSTR/0.6.2-foss-2018b-Python-3.6.6

</details>

HISAT2

Description: 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). Homepage: https://ccb.jhu.edu/software/hisat2/index.shtml

Installed versions: - HISAT2/2.1.0-foss-2018b

</details>

HMMER

Description: 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. Homepage: http://hmmer.org/

Installed versions: - HMMER/2.3.2-GCC-7.3.0-2.30 - HMMER/3.2.1-GCC-8.2.0-2.31.1 - HMMER/3.2.1-foss-2018b - HMMER/3.2.1-intel-2018b

</details>

htop

Description: An interactive process viewer for Unix Homepage: http://hisham.hm/htop/

Installed versions: - htop/2.2.0

</details>

HTSeq

Description: HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments. Homepage: https://github.com/simon-anders/htseq

Installed versions: - HTSeq/0.11.2-foss-2019a-Python-3.7.2

</details>

HTSlib

Description: A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix Homepage: http://www.htslib.org/

Installed versions: - HTSlib/1.9-GCC-7.3.0-2.30 - HTSlib/1.9-GCC-8.2.0-2.31.1 - HTSlib/1.9-foss-2018b - HTSlib/1.9-iccifort-2019.1.144-GCC-8.2.0-2.31.1 - HTSlib/1.9-intel-2018b

</details>

hwloc

Description: 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.

Homepage: https://www.open-mpi.org/projects/hwloc/

Installed versions: - hwloc/1.11.10-GCCcore-7.3.0 - hwloc/1.11.12-GCCcore-8.3.0

</details>

hypothesis

Description: 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. Homepage: https://github.com/HypothesisWorks/hypothesis

Installed versions: - hypothesis/4.5.0-fosscuda-2018b-Python-3.6.6

</details>

Hypre

Description: 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. Homepage: https://computation.llnl.gov/projects/hypre-scalable-linear-solvers-multigrid-methods

Installed versions: - Hypre/2.15.0-foss-2018b - Hypre/2.15.0-intel-2018b - Hypre/2.15.1-foss-2019a - Hypre/2.15.1-intel-2019a

</details>

icc

Description: Intel C and C++ compilers Homepage: http://software.intel.com/en-us/intel-compilers/

Installed versions: - icc/2018.1.163-GCC-6.4.0-2.28 - icc/2018.3.222-GCC-7.3.0-2.30 - icc/2019.1.144-GCC-8.2.0-2.31.1

</details>

iccifort

Description: Intel C, C++ & Fortran compilers Homepage: http://software.intel.com/en-us/intel-compilers/

Installed versions: - iccifort/2018.1.163-GCC-6.4.0-2.28 - iccifort/2018.3.222-GCC-7.3.0-2.30 - iccifort/2019.1.144-GCC-8.2.0-2.31.1 - iccifort/2019.5.281

</details>

iccifortcuda

Description: Intel C, C++ & Fortran compilers with CUDA toolkit Homepage: (none)

Installed versions: - iccifortcuda/2019a - iccifortcuda/2019b

</details>

ICU

Description: ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications. Homepage: http://site.icu-project.org/home

Installed versions: - ICU/61.1-GCCcore-7.3.0 - ICU/64.2-GCCcore-8.2.0 - ICU/64.2-GCCcore-8.3.0

</details>

ifort

Description: Intel Fortran compiler Homepage: http://software.intel.com/en-us/intel-compilers/

Installed versions: - ifort/2018.1.163-GCC-6.4.0-2.28 - ifort/2018.3.222-GCC-7.3.0-2.30 - ifort/2019.1.144-GCC-8.2.0-2.31.1

</details>

iimpi

Description: Intel C/C++ and Fortran compilers, alongside Intel MPI. Homepage: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/

Installed versions: - iimpi/2018a - iimpi/2018b - iimpi/2019a - iimpi/2019b

</details>

iimpic

Description: Intel C/C++ and Fortran compilers, alongside Intel MPI and CUDA. Homepage: (none)

Installed versions: - iimpic/2019a - iimpic/2019b

</details>

ImageMagick

Description: ImageMagick is a software suite to create, edit, compose, or convert bitmap images Homepage: https://www.imagemagick.org/

Installed versions: - ImageMagick/7.0.8-46-GCCcore-8.2.0 - ImageMagick/7.0.9-5-GCCcore-8.3.0

</details>

imkl

Description: 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. Homepage: https://software.intel.com/en-us/intel-mkl/

Installed versions: - imkl/2018.1.163-iimpi-2018a - imkl/2018.3.222-iimpi-2018b - imkl/2018.3.222-iompi-2018b - imkl/2019.1.144-iimpi-2019a - imkl/2019.1.144-iimpic-2019a - imkl/2019.5.281-iimpi-2019b - imkl/2019.5.281-iimpic-2019b

</details>

impi

Description: Intel MPI Library, compatible with MPICH ABI Homepage: https://software.intel.com/en-us/intel-mpi-library/

Installed versions: - impi/2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28 - impi/2018.3.222-iccifort-2018.3.222-GCC-7.3.0-2.30 - impi/2018.4.274-iccifort-2019.1.144-GCC-8.2.0-2.31.1 - impi/2018.4.274-iccifortcuda-2019a - impi/2018.5.288-iccifort-2019.5.281 - impi/2018.5.288-iccifortcuda-2019b

</details>

intel

Description: Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL). Homepage: https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain

Installed versions: - intel/2018a - intel/2018b - intel/2019a - intel/2019b

</details>

intelcuda

Description: Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL, with CUDA toolkit Homepage: (none)

Installed versions: - intelcuda/2019a - intelcuda/2019b

</details>

InterProScan

Description: InterProScan is a sequence analysis application (nucleotide and protein sequences) that combines different protein signature recognition methods into one resource. Homepage: http://www.ebi.ac.uk/interpro/

Installed versions: - InterProScan/5.34-73.0-intel-2019a

</details>

intltool

Description: intltool is a set of tools to centralize translation of many different file formats using GNU gettext-compatible PO files. Homepage: http://freedesktop.org/wiki/Software/intltool/

Installed versions: - intltool/0.51.0-GCCcore-7.3.0-Perl-5.28.0 - intltool/0.51.0-GCCcore-8.2.0 - intltool/0.51.0-GCCcore-8.3.0

</details>

iomkl

Description: Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI. Homepage: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/

Installed versions: - iomkl/2018b

</details>

iompi

Description: Intel C/C++ and Fortran compilers, alongside Open MPI. Homepage: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/

Installed versions: - iompi/2018b

</details>

ipyparallel

Description: ipyparallel is a Python package and collection of CLI scripts for controlling clusters for Jupyter Homepage: https://ipyparallel.readthedocs.io

Installed versions: - ipyparallel/6.2.4-foss-2018b-Python-3.6.6

</details>

ipyrad

Description: ipyrad is an interactive toolkit for assembly and analysis of restriction-site associated genomic data sets (e.g., RAD, ddRAD, GBS) for population genetic and phylogenetic studies. Homepage: https://ipyrad.readthedocs.io

Installed versions: - ipyrad/0.9.18-foss-2018b-Python-3.6.6

</details>

IPython

Description: IPython provides a rich architecture for interactive computing with: Powerful interactive shells (terminal and Qt-based). A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. Support for interactive data visualization and use of GUI toolkits. Flexible, embeddable interpreters to load into your own projects. Easy to use, high performance tools for parallel computing. Homepage: http://ipython.org/index.html

Installed versions: - IPython/5.8.0-foss-2018b-Python-2.7.15 - IPython/7.2.0-foss-2018b-Python-3.6.6

</details>

IQ-TREE

Description: Efficient phylogenomic software by maximum likelihood Homepage: http://www.iqtree.org/

Installed versions: - IQ-TREE/1.6.8-intel-2018b

</details>

ITK

Description: Insight Segmentation and Registration Toolkit (ITK) provides an extensive suite of software tools for registering and segmenting multidimensional imaging data. Homepage: https://itk.org

Installed versions: - ITK/4.13.1-foss-2018b-Python-3.6.6

</details>

JasPer

Description: 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.

Homepage: https://www.ece.uvic.ca/~frodo/jasper/

Installed versions: - JasPer/2.0.14-GCCcore-7.3.0 - JasPer/2.0.14-GCCcore-8.2.0 - JasPer/2.0.14-GCCcore-8.3.0

</details>

Java

Description: Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers. Homepage: http://openjdk.java.net

Installed versions: - Java/1.7.0_80 - Java/1.8.0_212 - Java/11.0.2

</details>

Jellyfish

Description: Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. Homepage: http://www.genome.umd.edu/jellyfish.html

Installed versions: - Jellyfish/2.2.10-foss-2018b - Jellyfish/2.3.0-GCC-8.2.0-2.31.1

</details>

jemalloc

Description: jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and scalable concurrency support. Homepage: http://jemalloc.net

Installed versions: - jemalloc/5.1.0-GCCcore-7.3.0 - jemalloc/5.2.0-GCCcore-8.2.0

</details>

Julia

Description: Julia as an open source high performance programming language. Homepage: https://julialang.org/

Installed versions: - Julia/1.1.1

</details>

Keras

Description: Keras is a minimalist, highly modular neural networks library, written in Python and capable of running on top of either TensorFlow or Theano. Homepage: https://keras.io/

Installed versions: - Keras/2.2.2-fosscuda-2018b-Python-3.6.6

</details>

khmer

Description: In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more Homepage: https://github.com/ged-lab/khmer/

Installed versions: - khmer/2.1.1-intel-2018b-Python-2.7.15

</details>

Kraken2

Description: 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. Homepage: http://www.ccb.jhu.edu/software/kraken2/

Installed versions: - Kraken2/2.0.7-beta-foss-2018b-Perl-5.28.0 - Kraken2/2.0.8-beta-foss-2018b-Perl-5.28.0

</details>

L_RNA_scaffolder

Description: L_RNA_scaffolder is a genome scaffolding tool with long trancriptome reads Homepage: https://github.com/CAFS-bioinformatics/L_RNA_scaffolder

Installed versions: - L_RNA_scaffolder/190530

</details>

LAMMPS

Description: LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a classical molecular dynamics simulation code designed to run efficiently on parallel computers. Homepage: http://lammps.sandia.gov/

Installed versions: - LAMMPS/7Aug19-foss-2018b-Python-2.7.15

</details>

libcerf

Description: 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.

Homepage: http://apps.jcns.fz-juelich.de/doku/sc/libcerf

Installed versions: - libcerf/1.7-GCCcore-7.3.0 - libcerf/1.11-GCCcore-8.2.0

</details>

libdap

Description: A C++ SDK which contains an implementation of DAP 2.0 and the development versions of DAP3, up to 3.4. This includes both Client- and Server-side support classes. Homepage: http://opendap.org/download/libdap

Installed versions: - libdap/3.20.3-GCCcore-7.3.0

</details>

libdrm

Description: Direct Rendering Manager runtime library. Homepage: http://dri.freedesktop.org

Installed versions: - libdrm/2.4.92-GCCcore-7.3.0 - libdrm/2.4.97-GCCcore-8.2.0 - libdrm/2.4.99-GCCcore-8.3.0

</details>

libevent

Description: 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.

Homepage: https://libevent.org/

Installed versions: - libevent/2.1.11-GCCcore-8.3.0

</details>

libffi

Description: The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run-time.

Homepage: https://sourceware.org/libffi/

Installed versions: - libffi/3.2.1-GCCcore-6.4.0 - libffi/3.2.1-GCCcore-7.3.0 - libffi/3.2.1-GCCcore-8.2.0 - libffi/3.2.1-GCCcore-8.3.0

</details>

libgd

Description: GD is an open source code library for the dynamic creation of images by programmers. Homepage: https://libgd.github.io/

Installed versions: - libgd/2.2.5-GCCcore-7.3.0 - libgd/2.2.5-GCCcore-8.2.0

</details>

libgeotiff

Description: Library for reading and writing coordinate system information from/to GeoTIFF files Homepage: https://directory.fsf.org/wiki/Libgeotiff

Installed versions: - libgeotiff/1.4.2-foss-2018b - libgeotiff/1.4.2-intel-2018b - libgeotiff/1.5.1-GCCcore-8.2.0 - libgeotiff/1.5.1-GCCcore-8.3.0

</details>

libGLU

Description: The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. Homepage: ftp://ftp.freedesktop.org/pub/mesa/glu/

Installed versions: - libGLU/9.0.0-GCCcore-8.2.0 - libGLU/9.0.0-foss-2018b - libGLU/9.0.0-intel-2018b - libGLU/9.0.1-GCCcore-8.3.0

</details>

libgpuarray

Description: Library to manipulate tensors on the GPU. Homepage: http://deeplearning.net/software/libgpuarray/

Installed versions: - libgpuarray/0.7.6-fosscuda-2018b-Python-3.6.6

</details>

libgtextutils

Description: ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream Homepage: http://hannonlab.cshl.edu/fastx_toolkit/

Installed versions: - libgtextutils/0.7-GCCcore-7.3.0

</details>

libharu

Description: libHaru is a free, cross platform, open source library for generating PDF files. Homepage: http://libharu.org/

Installed versions: - libharu/2.3.0-GCCcore-7.3.0 - libharu/2.3.0-intel-2018b

</details>

Libint

Description: 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. Homepage: https://sourceforge.net/p/libint/

Installed versions: - Libint/1.1.6-GCC-8.2.0-2.31.1 - Libint/1.1.6-iccifort-2019.1.144-GCC-8.2.0-2.31.1 - Libint/1.1.6-intel-2018a - Libint/1.1.6-intel-2018b

</details>

libjpeg-turbo

Description: 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.

Homepage: https://sourceforge.net/projects/libjpeg-turbo/

Installed versions: - libjpeg-turbo/2.0.0-GCCcore-7.3.0 - libjpeg-turbo/2.0.2-GCCcore-8.2.0 - libjpeg-turbo/2.0.3-GCCcore-8.3.0

</details>

libmatheval

Description: GNU libmatheval is a library (callable from C and Fortran) to parse and evaluate symbolic expressions input as text. Homepage: http://www.gnu.org/software/libmatheval/

Installed versions: - libmatheval/1.1.11-GCCcore-6.4.0 - libmatheval/1.1.11-GCCcore-7.3.0 - libmatheval/1.1.11-GCCcore-8.2.0

</details>

libpciaccess

Description: Generic PCI access library. Homepage: http://cgit.freedesktop.org/xorg/lib/libpciaccess/

Installed versions: - libpciaccess/0.14-GCCcore-7.3.0 - libpciaccess/0.14-GCCcore-8.3.0

</details>

libpng

Description: libpng is the official PNG reference library Homepage: http://www.libpng.org/pub/png/libpng.html

Installed versions: - libpng/1.2.58 - libpng/1.6.34-GCCcore-7.3.0 - libpng/1.6.36-GCCcore-8.2.0 - libpng/1.6.37-GCCcore-8.3.0

</details>

libreadline

Description: 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.

Homepage: https://tiswww.case.edu/php/chet/readline/rltop.html

Installed versions: - libreadline/7.0-GCCcore-7.3.0 - libreadline/8.0-GCCcore-8.2.0 - libreadline/8.0-GCCcore-8.3.0

</details>

libsigc++

Description: The libsigc++ package implements a typesafe callback system for standard C++. Homepage: https://libsigcplusplus.github.io/libsigcplusplus/

Installed versions: - libsigc++/2.10.2-GCCcore-8.2.0

</details>

libsndfile

Description: 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. Homepage: http://www.mega-nerd.com/libsndfile

Installed versions: - libsndfile/1.0.28-GCCcore-7.3.0 - libsndfile/1.0.28-GCCcore-8.2.0 - libsndfile/1.0.28-GCCcore-8.3.0

</details>

libsodium

Description: Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more.

Homepage: http://doc.libsodium.org/

Installed versions: - libsodium/1.0.16-GCCcore-7.3.0

</details>

LibTIFF

Description: tiff: Library and tools for reading and writing TIFF data files Homepage: http://www.remotesensing.org/libtiff/

Installed versions: - LibTIFF/4.0.9-GCCcore-7.3.0 - LibTIFF/4.0.9-intel-2018b - LibTIFF/4.0.10-GCCcore-8.2.0 - LibTIFF/4.0.10-GCCcore-8.3.0

</details>

libtool

Description: GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface.

Homepage: http://www.gnu.org/software/libtool

Installed versions: - libtool/2.4.6-GCCcore-6.4.0 - libtool/2.4.6-GCCcore-7.3.0 - libtool/2.4.6-GCCcore-8.2.0 - libtool/2.4.6-GCCcore-8.3.0

</details>

libunistring

Description: This library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard.

Homepage: http://www.gnu.org/software/libunistring/

Installed versions: - libunistring/0.9.7-GCCcore-6.4.0 - libunistring/0.9.10-GCCcore-7.3.0 - libunistring/0.9.10-GCCcore-8.2.0

</details>

libunwind

Description: 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 Homepage: https://www.nongnu.org/libunwind/

Installed versions: - libunwind/1.2.1-GCCcore-7.3.0 - libunwind/1.3.1-GCCcore-8.2.0 - libunwind/1.3.1-GCCcore-8.3.0

</details>

libxc

Description: Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals. Homepage: http://www.tddft.org/programs/octopus/wiki/index.php/Libxc

Installed versions: - libxc/4.2.3-intel-2018a - libxc/4.2.3-intel-2018b - libxc/4.3.4-GCC-8.2.0-2.31.1 - libxc/4.3.4-iccifort-2019.1.144-GCC-8.2.0-2.31.1

</details>

libxml++

Description: libxml++ is a C++ wrapper for the libxml XML parser library. Homepage: http://libxmlplusplus.sourceforge.net

Installed versions: - libxml++/2.40.1-GCCcore-8.2.0

</details>

libxml2

Description: Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform).

Homepage: http://xmlsoft.org/

Installed versions: - libxml2/2.9.8-GCCcore-7.3.0 - libxml2/2.9.8-GCCcore-8.2.0 - libxml2/2.9.9-GCCcore-8.3.0

</details>

libxslt

Description: Libxslt is the XSLT C library developed for the GNOME project (but usable outside of the Gnome platform). Homepage: http://xmlsoft.org/

Installed versions: - libxslt/1.1.32-GCCcore-7.3.0 - libxslt/1.1.33-GCCcore-8.2.0

</details>

libxsmm

Description: LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86). Homepage: https://github.com/hfp/libxsmm

Installed versions: - libxsmm/1.8.3-intel-2018a - libxsmm/1.10-GCC-8.2.0-2.31.1 - libxsmm/1.10-intel-2018b

</details>

libyaml

Description: LibYAML is a YAML parser and emitter written in C. Homepage: http://pyyaml.org/wiki/LibYAML

Installed versions: - libyaml/0.2.1-GCCcore-7.3.0 - libyaml/0.2.2-GCCcore-8.2.0

</details>

Description: LINKS is a genomics application for scaffolding genome assemblies with long reads Homepage: https://github.com/bcgsc/LINKS

Installed versions: - LINKS/1.8.7-GCC-8.2.0-2.31.1-Perl-5.28.1

</details>

LittleCMS

Description: Little CMS intends to be an OPEN SOURCE small-footprint color management engine, with special focus on accuracy and performance. Homepage: http://www.littlecms.com/

Installed versions: - LittleCMS/2.9-GCCcore-8.2.0 - LittleCMS/2.9-GCCcore-8.3.0

</details>

LLVM

Description: The LLVM Core libraries provide a modern source- and target-independent optimizer, along with code generation support for many popular CPUs (as well as some less common ones!) These libraries are built around a well specified code representation known as the LLVM intermediate representation ("LLVM IR"). The LLVM Core libraries are well documented, and it is particularly easy to invent your own language (or port an existing compiler) to use LLVM as an optimizer and code generator. Homepage: http://llvm.org/

Installed versions: - LLVM/6.0.0-GCCcore-7.3.0 - LLVM/6.0.1-GCCcore-7.3.0 - LLVM/7.0.1-GCCcore-8.2.0 - LLVM/9.0.0-GCCcore-8.3.0

</details>

LMDB

Description: 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. Homepage: https://symas.com/lmdb

Installed versions: - LMDB/0.9.22-GCCcore-7.3.0 - LMDB/0.9.23-GCCcore-8.2.0 - LMDB/0.9.24-GCCcore-8.3.0

</details>

Loter

Description: A Python (and soon R) package for local ancestry inference and haplotype phasing. Homepage: https://github.com/bcm-uga/Loter

Installed versions: - Loter/191204-foss-2019a-Python-2.7.15

</details>

lpsolve

Description: Mixed Integer Linear Programming (MILP) solver Homepage: https://sourceforge.net/projects/lpsolve/

Installed versions: - lpsolve/5.5.2.5-intel-2018b

</details>

lxml

Description: The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt. Homepage: http://lxml.de/

Installed versions: - lxml/4.2.5-intel-2018b-Python-3.6.6 - lxml/4.3.3-GCCcore-8.2.0

</details>

lz4

Description: 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. Homepage: https://lz4.github.io/lz4/

Installed versions: - lz4/1.9.1-GCCcore-8.2.0

</details>

LZO

Description: Portable lossless data compression library Homepage: http://www.oberhumer.com/opensource/lzo/

Installed versions: - LZO/2.10-GCCcore-8.2.0

</details>

M4

Description: 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.

Homepage: http://www.gnu.org/software/m4/m4.html

Installed versions: - M4/1.4.17 - M4/1.4.18 - M4/1.4.18-GCCcore-6.4.0 - M4/1.4.18-GCCcore-7.3.0 - M4/1.4.18-GCCcore-8.2.0 - M4/1.4.18-GCCcore-8.3.0

</details>

MACS2

Description: Model Based Analysis for ChIP-Seq data Homepage: https://github.com/taoliu/MACS/

Installed versions: - MACS2/2.1.2.1-foss-2018b-Python-2.7.15 - MACS2/2.1.2.1-intel-2018b-Python-2.7.15

</details>

MAFFT

Description: 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. Homepage: https://mafft.cbrc.jp/alignment/software/source.html

Installed versions: - MAFFT/7.427-intel-2018b-with-extensions - MAFFT/7.429-GCC-8.2.0-2.31.1-with-extensions

</details>

magma

Description: 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. Homepage: http://icl.cs.utk.edu/magma/

Installed versions: - magma/2.5.0-fosscuda-2018b

</details>

Maker

Description: A portable and easily configurable genome annotation pipeline. Homepage: https://www.yandell-lab.org/software/maker.html

Installed versions: - Maker/2.31.10-foss-2019a - Maker/3.01.02-beta-foss-2019a

</details>

Mako

Description: A super-fast templating language that borrows the best ideas from the existing templating languages Homepage: http://www.makotemplates.org

Installed versions: - Mako/1.0.7-foss-2018b-Python-2.7.15 - Mako/1.0.7-fosscuda-2018b-Python-3.6.6 - Mako/1.0.7-intel-2018b-Python-2.7.15 - Mako/1.0.8-GCCcore-8.2.0 - Mako/1.1.0-GCCcore-8.3.0

</details>

mapDamage

Description: 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. Homepage: https://www.biopython.org

Installed versions: - mapDamage/2.0.9-GCC-8.2.0-2.31.1-Python-2.7.15 - mapDamage/2.2.0-GCC-8.2.0-2.31.1-Python-3.7.2

</details>

MariaDB-connector-c

Description: MariaDB Connector/C is used to connect applications developed in C/C++ to MariaDB and MySQL databases. Homepage: https://downloads.mariadb.org/connector-c/

Installed versions: - MariaDB-connector-c/2.3.7-GCCcore-8.2.0 - MariaDB-connector-c/2.3.7-foss-2018b - MariaDB-connector-c/2.3.7-intel-2018b

</details>

MATIO

Description: matio is an C library for reading and writing Matlab MAT files. Homepage: http://sourceforge.net/projects/matio/

Installed versions: - MATIO/1.5.12-GCCcore-7.3.0

</details>

MATLAB

Description: 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. Homepage: http://www.mathworks.com/products/matlab

Installed versions: - MATLAB/2019a

</details>

matplotlib

Description: matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits. Homepage: https://matplotlib.org

Installed versions: - matplotlib/2.2.3-foss-2018b-Python-2.7.15 - matplotlib/2.2.3-fosscuda-2018b-Python-2.7.15 - matplotlib/2.2.3-intel-2018b-Python-2.7.15 - matplotlib/2.2.4-foss-2019a-Python-2.7.15 - matplotlib/2.2.4-intel-2019a-Python-2.7.15 - matplotlib/3.0.0-foss-2018b-Python-3.6.6 - matplotlib/3.0.0-intel-2018b-Python-3.6.6 - matplotlib/3.0.3-foss-2019a-Python-3.7.2 - matplotlib/3.0.3-intel-2019a-Python-3.7.2 - matplotlib/3.1.1-foss-2019b-Python-3.7.4

</details>

MCL

Description: 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. Homepage: http://micans.org/mcl/

Installed versions: - MCL/14.137-intel-2018b

</details>

MEGAHIT

Description: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph Homepage: https://github.com/voutcn/megahit

Installed versions: - MEGAHIT/1.1.4-foss-2018b-Python-3.6.6 - MEGAHIT/1.2.8-GCCcore-8.2.0

</details>

Mesa

Description: Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics. Homepage: https://www.mesa3d.org/

Installed versions: - Mesa/18.1.1-foss-2018b - Mesa/18.1.1-intel-2018b - Mesa/19.0.1-GCCcore-8.2.0 - Mesa/19.1.7-GCCcore-8.3.0

</details>

Meson

Description: Meson is a cross-platform build system designed to be both as fast and as user friendly as possible. Homepage: https://mesonbuild.com

Installed versions: - Meson/0.50.0-GCCcore-8.2.0-Python-3.7.2 - Meson/0.51.2-GCCcore-8.3.0-Python-3.7.4

</details>

MetaBAT

Description: An efficient tool for accurately reconstructing single genomes from complex microbial communities Homepage: https://bitbucket.org/berkeleylab/metabat

Installed versions: - MetaBAT/2.14-gompi-2019a

</details>

Metaxa2

Description: Metaxa2 -- Identifies Small Subunit (SSU) rRNAs and classifies them taxonomically Homepage: https://microbiology.se/software/metaxa2/

Installed versions: - Metaxa2/2.2-gompi-2019a

</details>

METIS

Description: METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.

Homepage: http://glaros.dtc.umn.edu/gkhome/metis/metis/overview

Installed versions: - METIS/5.1.0-GCCcore-7.3.0 - METIS/5.1.0-GCCcore-8.2.0 - METIS/5.1.0-GCCcore-8.3.0

</details>

Miniconda3

Description: 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.

Homepage: https://www.continuum.io/anaconda-overview

Installed versions: - Miniconda3/4.5.12 - Miniconda3/4.7.10

</details>

minimap2

Description: 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. Homepage: https://github.com/lh3/minimap2

Installed versions: - minimap2/2.13-foss-2018b - minimap2/2.17-GCC-8.2.0-2.31.1

</details>

MIRA

Description: MIRA is a whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina), IonTorrent data and PacBio (the latter at the moment only CCS and error-corrected CLR reads). Homepage: https://sourceforge.net/projects/mira-assembler/

Installed versions: - MIRA/4.9.6-foss-2018b

</details>

MITObim

Description: The MITObim procedure (mitochondrial baiting and iterative mapping) represents an efficient approach to assembling novel mitochondrial genomes of non-model organisms directly from total genomic DNA derived NGS reads. Homepage: https://github.com/chrishah/MITObim

Installed versions: - MITObim/1.9.1-foss-2018b-Perl-5.28.0

</details>

MITOS

Description: MITOS is a pipeline designed to compute a consistent de novo annotation of the mitogenomic sequences. Homepage: https://gitlab.com/Bernt/MITOS

Installed versions: - MITOS/2.0.2-foss-2019a-Python-2.7.15

</details>

Mothur

Description: Mothur is a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. Homepage: https://www.mothur.org/

Installed versions: - Mothur/1.41.0-foss-2018b-Python-2.7.15 - Mothur/1.43.0-foss-2019a-Python-3.7.2

</details>

MPFR

Description: The MPFR library is a C library for multiple-precision floating-point computations with correct rounding.

Homepage: http://www.mpfr.org

Installed versions: - MPFR/4.0.1-GCCcore-7.3.0 - MPFR/4.0.2-GCCcore-8.2.0

</details>

MrBayes

Description: MrBayes is a program for the Bayesian estimation of phylogeny. Homepage: http://mrbayes.csit.fsu.edu

Installed versions: - MrBayes/3.2.6-foss-2018b

</details>

MrBayes5D

Description: A modified version of MrBayes. Homepage: http://mrbayes.csit.fsu.edu

Installed versions: - MrBayes5D/3.2.6-foss-2018b

</details>

MSMC

Description: This software implements the multiple sequentially Markovian coalescent (MSMC), a method to infer population size and gene flow from multiple genome sequences. Homepage: https://github.com/stschiff/msmc

Installed versions: - MSMC/1.1.0-linux64

</details>

MSMC2

Description: This program implements MSMC2, a method to infer population size history and population separation history from whole genome sequencing data. Homepage: https://github.com/stschiff/msmc2

Installed versions: - MSMC2/2.1.2-linux64

</details>

MUMmer

Description: MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. AMOS makes use of it. Homepage: http://mummer.sourceforge.net/

Installed versions: - MUMmer/4.0.0beta2-foss-2018b

</details>

MUSCLE

Description: 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. Homepage: http://drive5.com/muscle/

Installed versions: - MUSCLE/3.8.31-foss-2018b - MUSCLE/3.8.31-intel-2018b

</details>

NAMD

Description: NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Homepage: http://www.ks.uiuc.edu/Research/namd/

Installed versions: - NAMD/2.13-foss-2018b-mpi

</details>

NASM

Description: NASM: General-purpose x86 assembler Homepage: https://www.nasm.us/

Installed versions: - NASM/2.13.03-GCCcore-7.3.0 - NASM/2.14.02-GCCcore-8.2.0 - NASM/2.14.02-GCCcore-8.3.0

</details>

NBO7

Description: NBO7 is the most recent version of a program suite aimed at analysing natural bond order in different outputs: The NBO program performs the analysis of a many-electron molecular wavefunction in terms of localized electron-pair bonding units. Homepage: http://nbo6.chem.wisc.edu

Installed versions: - NBO7/09-Sep-2019-intel-2018b

</details>

ncbi-vdb

Description: The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. Homepage: https://github.com/ncbi/ncbi-vdb

Installed versions: - ncbi-vdb/2.9.3-foss-2018b

</details>

NCCL

Description: The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective communication primitives that are performance optimized for NVIDIA GPUs. Homepage: https://developer.nvidia.com/nccl

Installed versions: - NCCL/2.4.8-CUDA-10.0 - NCCL/2.4.8-gcccuda-2018b - NCCL/2.4.8-gcccuda-2019a - NCCL/2.4.8-gcccuda-2019b

</details>

ncdf4

Description: ncdf4: Interface to Unidata netCDF (version 4 or earlier) format data files Homepage: http://cran.r-project.org/web/packages/ncdf4

Installed versions: - ncdf4/1.16.1-foss-2019a-R-3.6.0

</details>

ncdu

Description: Ncdu is a disk usage analyzer with an ncurses interface. It is designed to find space hogs on a remote server where you don't have an entire graphical setup available, but it is a useful tool even on regular desktop systems. Ncdu aims to be fast, simple and easy to use, and should be able to run in any minimal POSIX-like environment with ncurses installed. Homepage: https://dev.yorhel.nl/ncdu

Installed versions: - ncdu/1.14-GCCcore-7.3.0

</details>

NCO

Description: manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5 Homepage: http://nco.sourceforge.net

Installed versions: - NCO/4.7.9-foss-2018b - NCO/4.7.9-intel-2018b

</details>

ncurses

Description: The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses. Homepage: http://www.gnu.org/software/ncurses/

Installed versions: - ncurses/6.0 - ncurses/6.0-GCCcore-7.3.0 - ncurses/6.1 - ncurses/6.1-GCCcore-7.3.0 - ncurses/6.1-GCCcore-8.2.0 - ncurses/6.1-GCCcore-8.3.0

</details>

ncview

Description: Ncview is a visual browser for netCDF format files. Typically you would use ncview to get a quick and easy, push-button look at your netCDF files. You can view simple movies of the data, view along various dimensions, take a look at the actual data values, change color maps, invert the data, etc. Homepage: http://meteora.ucsd.edu/~pierce/ncview_home_page.html

Installed versions: - ncview/2.1.7-foss-2018b - ncview/2.1.7-intel-2018b

</details>

netCDF

Description: NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. Homepage: https://www.unidata.ucar.edu/software/netcdf/

Installed versions: - netCDF/4.6.1-foss-2018b - netCDF/4.6.1-fosscuda-2018b - netCDF/4.6.1-intel-2018b - netCDF/4.6.2-gompi-2019a - netCDF/4.6.2-iimpi-2019a - netCDF/4.7.1-gompi-2019b - netCDF/4.7.1-iimpi-2019b

</details>

netCDF-Fortran

Description: NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. Homepage: http://www.unidata.ucar.edu/software/netcdf/

Installed versions: - netCDF-Fortran/4.4.4-foss-2018b - netCDF-Fortran/4.4.4-fosscuda-2018b - netCDF-Fortran/4.4.4-intel-2018b - netCDF-Fortran/4.4.5-gompi-2019a - netCDF-Fortran/4.4.5-iimpi-2019a

</details>

netcdf4-python

Description: Python/numpy interface to netCDF. Homepage: https://unidata.github.io/netcdf4-python/

Installed versions: - netcdf4-python/1.4.1-foss-2018b-Python-3.6.6 - netcdf4-python/1.4.1-intel-2018b-Python-3.6.6

</details>

nettle

Description: Nettle is a cryptographic library that is designed to fit easily in more or less any context: In crypto toolkits for object-oriented languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, or even in kernel space. Homepage: http://www.lysator.liu.se/~nisse/nettle/

Installed versions: - nettle/3.4-foss-2018b - nettle/3.4-intel-2018b - nettle/3.4.1-GCCcore-8.2.0 - nettle/3.5.1-GCCcore-8.3.0

</details>

NGS

Description: NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. Homepage: https://github.com/ncbi/ngs

Installed versions: - NGS/2.9.3-foss-2018b-Java-1.8

</details>

NGSadmix

Description: NGSadmix is a tool for finding admixture proportions from NGS data, based on genotype likelihoods. Homepage: http://www.popgen.dk/software/index.php/NgsAdmix

Installed versions: - NGSadmix/32-GCC-7.3.0-2.30

</details>

ngsDist

Description: A program to estimate pairwise genetic distances directly, taking the uncertainty of genotype's assignation into account. Homepage: https://github.com/fgvieira/ngsDist

Installed versions: - ngsDist/191118-GCC-8.2.0-2.31.1

</details>

ngsLD

Description: a program to estimate pairwise linkage disequilibrium (LD) taking the uncertainty of genotype's assignation into account. Homepage: https://github.com/fgvieira/ngsLD

Installed versions: - ngsLD/191108-GCC-8.2.0-2.31.1

</details>

ngsTools

Description: A collection of programs for population genetics analyses from NGS data, taking into account data statistical uncertainty. Homepage: https://github.com/mfumagalli/ngsTools

Installed versions: - ngsTools/190624-GCC-8.2.0-2.31.1

</details>

Ninja

Description: Ninja is a small build system with a focus on speed. Homepage: https://ninja-build.org/

Installed versions: - Ninja/1.8.2-fosscuda-2018b - Ninja/1.9.0-GCCcore-8.2.0 - Ninja/1.9.0-GCCcore-8.3.0

</details>

NLopt

Description: 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. Homepage: http://ab-initio.mit.edu/wiki/index.php/NLopt

Installed versions: - NLopt/2.4.2-GCCcore-7.3.0 - NLopt/2.6.1-GCCcore-8.2.0 - NLopt/2.6.1-GCCcore-8.3.0

</details>

NOVOPlasty

Description: NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes. Homepage: https://github.com/ndierckx/NOVOPlasty

Installed versions: - NOVOPlasty/3.7-GCCcore-8.3.0 - NOVOPlasty/3.7-intel-2018b-Perl-5.28.0

</details>

NSPR

Description: Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level and libc-like functions. Homepage: https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSPR

Installed versions: - NSPR/4.20-GCCcore-7.3.0 - NSPR/4.21-GCCcore-8.2.0 - NSPR/4.21-GCCcore-8.3.0

</details>

NSS

Description: Network Security Services (NSS) is a set of libraries designed to support cross-platform development of security-enabled client and server applications. Homepage: https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSS

Installed versions: - NSS/3.39-GCCcore-7.3.0 - NSS/3.42.1-GCCcore-8.2.0 - NSS/3.45-GCCcore-8.3.0

</details>

ntCard

Description: ntCard is a streaming algorithm for cardinality estimation in genomics datasets. Homepage: https://github.com/bcgsc/ntCard

Installed versions: - ntCard/1.1.1-GCCcore-8.2.0

</details>

ntEdit

Description: Fast, lightweight, scalable genome sequence polishing & snv detection. Homepage: https://github.com/bcgsc/ntEdit

Installed versions: - ntEdit/1.3.1-GCCcore-8.2.0

</details>

ntHits

Description: ntHits is a method for identifying reapeats in high-throughput DNA sequencing data. Homepage: https://github.com/bcgsc/ntHits

Installed versions: - ntHits/0.0.1-GCCcore-8.2.0

</details>

numactl

Description: 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.

Homepage: http://oss.sgi.com/projects/libnuma/

Installed versions: - numactl/2.0.11-GCCcore-7.3.0 - numactl/2.0.12-GCCcore-8.3.0

</details>

numba

Description: 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. Homepage: http://numba.pydata.org/

Installed versions: - numba/0.41.0-foss-2018b-Python-3.6.6 - numba/0.41.0-intel-2018b-Python-2.7.15

</details>

numexpr

Description: 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. Homepage: https://numexpr.readthedocs.io

Installed versions: - numexpr/2.7.0-foss-2019a

</details>

NVidia

Description: This module makes NVidia drivers available to EasyBuild softwawre. Homepage: https://www.nvidia.com/

Installed versions: - NVidia/1.0

</details>

NWChem

Description: NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. NWChem software can handle: biomolecules, nanostructures, and solid-state; from quantum to classical, and all combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of processors; properties and relativity. Homepage: http://www.nwchem-sw.org

Installed versions: - NWChem/6.8.1.revision133-intel-2018b-2018-06-14-Python-2.7.15

</details>

OBITools

Description: The OBITools package is a set of programs specifically designed for analyzing NGS data in a DNA metabarcoding context, taking into account taxonomic information. Homepage: https://pythonhosted.org/OBITools/welcome.html

Installed versions: - OBITools/1.2.12-foss-2018b-Python-2.7.15

</details>

OpenBLAS

Description: OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. Homepage: http://xianyi.github.com/OpenBLAS/

Installed versions: - OpenBLAS/0.3.1-GCC-7.3.0-2.30 - OpenBLAS/0.3.5-GCC-8.2.0-2.31.1 - OpenBLAS/0.3.7-GCC-8.3.0

</details>

OpenFOAM

Description: OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. Homepage: http://www.openfoam.org/

Installed versions: - OpenFOAM/6-foss-2018b

</details>

OpenMPI

Description: The Open MPI Project is an open source MPI-3 implementation. Homepage: https://www.open-mpi.org/

Installed versions: - OpenMPI/3.1.1-GCC-7.3.0-2.30 - OpenMPI/3.1.1-gcccuda-2018b - OpenMPI/3.1.1-iccifort-2018.3.222-GCC-7.3.0-2.30 - OpenMPI/3.1.3-GCC-8.2.0-2.31.1 - OpenMPI/3.1.3-GCC-8.2.0-2.31.1-hpcx_2.4 - OpenMPI/3.1.3-GCC-8.2.0-2.31.1-hpcx_2.5 - OpenMPI/3.1.4-GCC-8.3.0 - OpenMPI/3.1.4-PGI-19.9-GCC-8.3.0

</details>

OpenPGM

Description: OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM) specification in RFC 3208 available at www.ietf.org. PGM is a reliable and scalable multicast protocol that enables receivers to detect loss, request retransmission of lost data, or notify an application of unrecoverable loss. PGM is a receiver-reliable protocol, which means the receiver is responsible for ensuring all data is received, absolving the sender of reception responsibility.

Homepage: http://code.google.com/p/openpgm/

Installed versions: - OpenPGM/5.2.122-GCCcore-7.3.0

</details>

ORCA

Description: 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. Homepage: https://orcaforum.kofo.mpg.de

Installed versions: - ORCA/4.2.0-gompi-2019b

</details>

OrthoMCL

Description: OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences. Homepage: http://orthomcl.org/

Installed versions: - OrthoMCL/2.0.9-intel-2018b-Perl-5.28.0

</details>

p7zip

Description: 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. Homepage: http://p7zip.sourceforge.net/

Installed versions: - p7zip/16.02-intel-2018a

</details>

PALEOMIX

Description: The PALEOMIX pipelines are a set of pipelines and tools designed to aid the rapid processing of High-Throughput Sequencing (HTS) data. Homepage: https://github.com/MikkelSchubert/paleomix

Installed versions: - PALEOMIX/1.2.14-GCC-8.2.0-2.31.1-Python-2.7.15

</details>

PAML

Description: PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Homepage: http://abacus.gene.ucl.ac.uk/software/paml.html

Installed versions: - PAML/4.9i-GCC-7.3.0-2.30

</details>

Pango

Description: Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x. Homepage: http://www.pango.org/

Installed versions: - Pango/1.42.4-foss-2018b - Pango/1.43.0-GCCcore-8.2.0

</details>

parallel

Description: parallel: Build and execute shell commands in parallel Homepage: https://savannah.gnu.org/projects/parallel/

Installed versions: - parallel/20190622-GCCcore-8.2.0 - parallel/20190922-GCCcore-8.3.0

</details>

ParaView

Description: ParaView is a scientific parallel visualizer. Homepage: http://www.paraview.org

Installed versions: - ParaView/5.4.1-foss-2018b-mpi - ParaView/5.5.2-foss-2018b-mpi

</details>

ParMETIS

Description: ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes. Homepage: http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview

Installed versions: - ParMETIS/4.0.3-foss-2018b - ParMETIS/4.0.3-gompi-2019a - ParMETIS/4.0.3-iimpi-2019a - ParMETIS/4.0.3-intel-2018b

</details>

parsyncfp

Description: Parallel rsync wrapper for large data transfers Homepage: http://moo.nac.uci.edu/~hjm/parsync/

Installed versions: - parsyncfp/1.61

</details>

patchelf

Description: PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables. Homepage: http://nixos.org/patchelf.html

Installed versions: - patchelf/0.9-GCCcore-7.3.0 - patchelf/0.10-GCCcore-8.2.0

</details>

PCAngsd

Description: PCAngsd, which estimates the covariance matrix for low depth NGS data in an iterative procedure based on genotype likelihoods and is able to perform multiple population genetic analyses in heterogeneous populations. Homepage: http://www.popgen.dk/software/index.php/PCAngsd

Installed versions: - PCAngsd/0.98-foss-2019a-Python-2.7.15 - PCAngsd/200115-foss-2019a-Python-2.7.15

</details>

PCRE

Description: The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.

Homepage: https://www.pcre.org/

Installed versions: - PCRE/8.41-GCCcore-7.3.0 - PCRE/8.43-GCCcore-8.2.0 - PCRE/8.43-GCCcore-8.3.0

</details>

PCRE2

Description: The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.

Homepage: https://www.pcre.org/

Installed versions: - PCRE2/10.33-GCCcore-8.3.0

</details>

Perl

Description: Larry Wall's Practical Extraction and Report Language Homepage: https://www.perl.org/

Installed versions: - Perl/5.28.0-GCCcore-7.3.0 - Perl/5.28.1-GCCcore-8.2.0 - Perl/5.30.0-GCCcore-8.3.0

</details>

PETSc

Description: 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. Homepage: http://www.mcs.anl.gov/petsc

Installed versions: - PETSc/3.11.0-foss-2018b - PETSc/3.11.0-intel-2018b - PETSc/3.11.1-foss-2018b - PETSc/3.11.1-foss-2019a - PETSc/3.11.1-intel-2018b - PETSc/3.11.1-intel-2019a

</details>

petsc4py

Description: petsc4py are Python bindings for PETSc, the Portable, Extensible Toolchain for Scientific Computation. Homepage: https://bitbucket.org/petsc/petsc4py

Installed versions: - petsc4py/3.11.0-foss-2018b-Python-3.6.6

</details>

PGDSpider

Description: An automated data conversion tool for connecting population genetics and genomics programs Homepage: http://cmpg.unibe.ch/software/PGDSpider/

Installed versions: - PGDSpider/2.1.1.5-Java-1.8

</details>

PGI

Description: C, C++ and Fortran compilers from The Portland Group Homepage: http://www.pgroup.com/

Installed versions: - PGI/19.9-GCC-8.3.0

</details>

phonopy

Description: Phonopy is an open source package of phonon calculations based on the supercell approach. Homepage: http://atztogo.github.io/phonopy/

Installed versions: - phonopy/1.14.2-intel-2018b-Python-3.6.6 - phonopy/2.2.0-intel-2019a-Python-3.7.2

</details>

PhyloBayes-MPI

Description: A Bayesian software for phylogenetic reconstruction using mixture models Homepage: https://github.com/bayesiancook/pbmpi

Installed versions: - PhyloBayes-MPI/1.8-intel-2018b

</details>

picard

Description: A set of tools (in Java) for working with next generation sequencing data in the BAM format. Homepage: https://sourceforge.net/projects/picard

Installed versions: - picard/2.18.27-Java-1.8 - picard/2.21.1-Java-11

</details>

pigz

Description: 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.

Homepage: http://zlib.net/pigz/

Installed versions: - pigz/2.4-GCCcore-7.3.0 - pigz/2.4-GCCcore-8.2.0

</details>

Pillow

Description: Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors. Homepage: http://pillow.readthedocs.org/

Installed versions: - Pillow/5.3.0-foss-2018b-Python-3.6.6 - Pillow/5.3.0-intel-2018b-Python-2.7.15 - Pillow/6.0.0-GCCcore-8.2.0

</details>

Pilon

Description: Pilon is an automated genome assembly improvement and variant detection tool Homepage: https://github.com/broadinstitute/pilon

Installed versions: - Pilon/1.23-Java-11

</details>

Pindel

Description: Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads. Homepage: http://gmt.genome.wustl.edu/packages/pindel/

Installed versions: - Pindel/0.2.5b9-20170508-GCC-7.3.0-2.30

</details>

pixman

Description: 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.

Homepage: http://www.pixman.org/

Installed versions: - pixman/0.34.0-GCCcore-7.3.0 - pixman/0.38.0-GCCcore-8.2.0 - pixman/0.38.4-GCCcore-8.3.0

</details>

pkg-config

Description: pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the correct compiler options on the command line so an application can use gcc -o test test.c pkg-config --libs --cflags glib-2.0 for instance, rather than hard-coding values on where to find glib (or other libraries).

Homepage: https://www.freedesktop.org/wiki/Software/pkg-config/

Installed versions: - pkg-config/0.29.2-GCCcore-7.3.0 - pkg-config/0.29.2-GCCcore-8.2.0 - pkg-config/0.29.2-GCCcore-8.3.0

</details>

pkgconfig

Description: pkgconfig is a Python module to interface with the pkg-config command line tool Homepage: https://github.com/matze/pkgconfig

Installed versions: - pkgconfig/1.3.1-foss-2018b-Python-3.6.6 - pkgconfig/1.3.1-fosscuda-2018b-Python-3.6.6 - pkgconfig/1.3.1-intel-2018b-Python-3.6.6 - pkgconfig/1.5.1-GCCcore-8.2.0-python - pkgconfig/1.5.1-GCCcore-8.3.0-Python-3.7.4

</details>

Description: Whole-genome association analysis toolset Homepage: https://www.cog-genomics.org/plink/1.9/

Installed versions: - PLINK/1.9b_6.13-x86_64 - PLINK/2.00-alpha1-x86_64

</details>

PLUMED

Description: 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.

Homepage: http://www.plumed-code.org

Installed versions: - PLUMED/2.4.0-intel-2018a - PLUMED/2.5.0-foss-2018b-Python-2.7.15 - PLUMED/2.5.0-fosscuda-2018b-Python-2.7.15 - PLUMED/2.5.1-foss-2019a - PLUMED/2.5.1-intel-2019a

</details>

PLY

Description: PLY is yet another implementation of lex and yacc for Python. Homepage: http://www.dabeaz.com/ply/

Installed versions: - PLY/3.11-foss-2018b-Python-3.6.6

</details>

pompi

Description: Toolchain with PGI C, C++ and Fortran compilers, alongside OpenMPI. Homepage: http://www.pgroup.com/index.htm

Installed versions: - pompi/2019.09

</details>

PoPoolation2

Description: PoPoolation2 allows to compare allele frequencies for SNPs between two or more populations and to identify significant differences. Homepage: https://sourceforge.net/p/popoolation2/wiki/Main/

Installed versions: - PoPoolation2/1201-foss-2019a

</details>

pplacer

Description: 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. Homepage: http://matsen.fhcrc.org/pplacer/

Installed versions: - pplacer/1.1.alpha19

</details>

preseq

Description: Software for predicting library complexity and genome coverage in high-throughput sequencing. Homepage: http://smithlabresearch.org/software/preseq

Installed versions: - preseq/2.0.3-foss-2018b

</details>

prodigal

Description: 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. Homepage: https://github.com/hyattpd/Prodigal/

Installed versions: - prodigal/2.6.3-GCCcore-7.3.0 - prodigal/2.6.3-GCCcore-8.2.0

</details>

PROJ

Description: Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates Homepage: https://proj.org

Installed versions: - PROJ/5.0.0-foss-2018b - PROJ/5.0.0-intel-2018b - PROJ/6.0.0-GCCcore-8.2.0 - PROJ/6.2.1-GCCcore-8.3.0

</details>

prokka

Description: Prokka is a software tool for the rapid annotation of prokaryotic genomes. Homepage: https://www.vicbioinformatics.com/software.prokka.shtml

Installed versions: - prokka/1.13.4-foss-2018b - prokka/1.14.5-gompi-2019b

</details>

protobuf

Description: Google Protocol Buffers Homepage: https://github.com/google/protobuf/

Installed versions: - protobuf/3.6.1-GCCcore-7.3.0 - protobuf/3.10.0-GCCcore-8.3.0

</details>

psmc

Description: This software package infers population size history from a diploid sequence using the Pairwise Sequentially Markovian Coalescent (PSMC) model. Homepage: https://github.com/lh3/psmc

Installed versions: - psmc/0.6.5-foss-2018b

</details>

Purge_Haplotigs

Description: Pipeline to help with curating heterozygous diploid genome assemblies Homepage: https://bitbucket.org/mroachawri/purge_haplotigs/src/master/

Installed versions: - Purge_Haplotigs/1.0.4-foss-2018b-Perl-5.28.0

</details>

pybind11

Description: 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. Homepage: https://pybind11.readthedocs.io

Installed versions: - pybind11/2.2.4-foss-2018b-Python-3.6.6 - pybind11/2.4.3-GCCcore-8.3.0-Python-3.7.4

</details>

Pysam

Description: 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. Homepage: https://github.com/pysam-developers/pysam

Installed versions: - Pysam/0.15.2-GCC-8.2.0-2.31.1 - Pysam/0.15.2-iccifort-2019.1.144-GCC-8.2.0-2.31.1 - Pysam/0.15.3-GCC-8.3.0 - Pysam/0.15.3-iccifort-2019.5.281

</details>

PyTables

Description: 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. Homepage: http://www.pytables.org

Installed versions: - PyTables/3.5.2-foss-2019a

</details>

pytest

Description: pytest: simple powerful testing with Python Homepage: http://pytest.org

Installed versions: - pytest/4.4.0-foss-2018b-Python-3.6.6

</details>

Python

Description: Python is a programming language that lets you work more quickly and integrate your systems more effectively. Homepage: http://python.org/

Installed versions: - Python/2.7.15-GCCcore-7.3.0-bare - Python/2.7.15-GCCcore-8.2.0 - Python/2.7.15-foss-2018b - Python/2.7.15-fosscuda-2018b - Python/2.7.15-intel-2018b - Python/2.7.16-GCCcore-8.3.0 - Python/3.6.6-foss-2018b - Python/3.6.6-fosscuda-2018b - Python/3.6.6-intel-2018b - Python/3.7.2-GCCcore-8.2.0 - Python/3.7.4-GCCcore-8.3.0

</details>

PyTorch

Description: Tensors and Dynamic neural networks in Python with strong GPU acceleration. PyTorch is a deep learning framework that puts Python first. Homepage: http://pytorch.org/

Installed versions: - PyTorch/1.0.1-fosscuda-2018b-Python-3.6.6

</details>

PyYAML

Description: PyYAML is a YAML parser and emitter for the Python programming language. Homepage: https://pypi.python.org/pypi/PyYAML/

Installed versions: - PyYAML/3.13-fosscuda-2018b-Python-3.6.6 - PyYAML/3.13-intel-2018b-Python-3.6.6 - PyYAML/5.1-GCCcore-8.2.0

</details>

QIIME2

Description: QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data. Homepage: http://qiime2.org/

Installed versions: - QIIME2/2019.4 - QIIME2/2019.7

</details>

Qt5

Description: Qt is a comprehensive cross-platform C++ application framework. Homepage: https://qt.io/

Installed versions: - Qt5/5.10.1-foss-2018b - Qt5/5.11.2-foss-2018b-nvidia - Qt5/5.12.3-GCCcore-8.2.0 - Qt5/5.13.1-GCCcore-8.3.0

</details>

QuantumESPRESSO

Description: Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft).

Homepage: https://www.quantum-espresso.org

Installed versions: - QuantumESPRESSO/6.4.1-intel-2019a

</details>

QUAST

Description: 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. Homepage: https://github.com/ablab/quast

Installed versions: - QUAST/5.0.2-foss-2018b-Python-2.7.15

</details>

Qwt

Description: The Qwt library contains GUI Components and utility classes which are primarily useful for programs with a technical background. Homepage: http://qwt.sourceforge.net/

Installed versions: - Qwt/6.1.4-GCCcore-8.2.0

</details>

R

Description: R is a free software environment for statistical computing and graphics. Homepage: https://www.r-project.org/

Installed versions: - R/3.5.1-foss-2018b - R/3.5.1-intel-2018b - R/3.6.0-foss-2019a - R/3.6.0-intel-2019a - R/3.6.2-foss-2019b

</details>

R-bundle-Bioconductor

Description: R is a free software environment for statistical computing and graphics. Homepage: http://www.r-project.org/

Installed versions: - R-bundle-Bioconductor/3.8-foss-2018b-R-3.5.1 - R-bundle-Bioconductor/3.8-intel-2018b-R-3.5.1 - R-bundle-Bioconductor/3.9-foss-2019a-R-3.6.0

</details>

RADProc

Description: An algorithm and software package that streamlines and accelerates de novo locus formation and catalog building by eliminating redundancies and using a highly efficient method for nucleotide distance calculation. Homepage: https://github.com/beiko-lab/RADProc

Installed versions: - RADProc/191206-GCCcore-8.2.0

</details>

RAxML

Description: RAxML search algorithm for maximum likelihood based inference of phylogenetic trees. Homepage: https://github.com/stamatak/standard-RAxML

Installed versions: - RAxML/8.2.12-foss-2018b-hybrid-avx2 - RAxML/8.2.12-intel-2018b-hybrid-avx2

</details>

RAxML-NG

Description: A phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. Homepage: https://github.com/amkozlov/raxml-ng

Installed versions: - RAxML-NG/191127-foss-2019a

</details>

re2c

Description: 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. Homepage: https://re2c.org/

Installed versions: - re2c/1.2.1-GCCcore-8.3.0

</details>

Reapr

Description: A tool that evaluates the accuracy of a genome assembly using mapped paired end reads, without the use of a reference genome for comparison. Homepage: https://www.sanger.ac.uk/science/tools/reapr

Installed versions: - Reapr/1.0.18-foss-2018b - Reapr/1.0.18-foss-2019a

</details>

RECON

Description: De Novo Repeat Finder. Homepage: http://www.repeatmasker.org/RepeatModeler/

Installed versions: - RECON/1.08-foss-2019a

</details>

Relate

Description: Software to estimate genome-wide genealogies for thousands of samples. Homepage: https://myersgroup.github.io/relate/

Installed versions: - Relate/1.0.17

</details>

RepeatMasker

Description: RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. Homepage: http://www.repeatmasker.org/

Installed versions: - RepeatMasker/4.0.9-p2-gompi-2019a-HMMER

</details>

RepeatModeler

Description: A de novo transposable element (TE) family identification and modeling package. Homepage: http://www.repeatmasker.org/RepeatModeler/

Installed versions: - RepeatModeler/2.0.1-foss-2019a

</details>

RepeatScout

Description: De Novo Repeat Finder. Homepage: http://www.repeatmasker.org/RepeatModeler/

Installed versions: - RepeatScout/1.0.6-foss-2019a

</details>

RevBayes

Description: RevBayes provides an interactive environment for statistical computation in phylogenetics Homepage: https://revbayes.github.io

Installed versions: - RevBayes/1.0.12-foss-2019b

</details>

RMBlast

Description: 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. Homepage: http://www.repeatmasker.org/RMBlast.html

Installed versions: - RMBlast/2.10.0-foss-2019a

</details>

RNAmmer

Description: RNAmmer predicts ribosomal RNA genes in full genome sequences Homepage: http://www.cbs.dtu.dk/services/RNAmmer/

Installed versions: - RNAmmer/1.2-GCC-7.3.0-2.30

</details>

ROHan

Description: ROHan is a Bayesian framework to estimate local rates of heterozygosity, infer runs of homozygosity (ROH) and compute global rates of heterozygosity. Homepage: https://github.com/grenaud/ROHan

Installed versions: - ROHan/200110-GCC-8.2.0-2.31.1

</details>

RSEM

Description: RNA-Seq by Expectation-Maximization Homepage: http://deweylab.github.io/RSEM/

Installed versions: - RSEM/1.3.2-foss-2018b

</details>

Ruby

Description: 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. Homepage: https://www.ruby-lang.org

Installed versions: - Ruby/2.6.3-GCCcore-8.2.0

</details>

Salmon

Description: Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. Homepage: https://github.com/COMBINE-lab/salmon

Installed versions: - Salmon/1.0.0-gompi-2019a

</details>

SAMtools

Description: SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. Homepage: http://www.htslib.org/

Installed versions: - SAMtools/1.9-GCC-7.3.0-2.30 - SAMtools/1.9-GCC-8.2.0-2.31.1 - SAMtools/1.9-foss-2018b - SAMtools/1.9-iccifort-2019.1.144-GCC-8.2.0-2.31.1 - SAMtools/1.9-intel-2018b

</details>

ScaLAPACK

Description: The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers. Homepage: http://www.netlib.org/scalapack/

Installed versions: - ScaLAPACK/2.0.2-gompi-2018b-OpenBLAS-0.3.1 - ScaLAPACK/2.0.2-gompi-2019a-OpenBLAS-0.3.5 - ScaLAPACK/2.0.2-gompi-2019b - ScaLAPACK/2.0.2-gompic-2018b-OpenBLAS-0.3.1

</details>

scikit-allel

Description: This package provides utilities for exploratory analysis of large scale genetic variation data. It is based on numpy, scipy and other general-purpose Python scientific libraries. Homepage: http://scikit-allel.readthedocs.io/en/latest/

Installed versions: - scikit-allel/1.2.1-foss-2019a-Python-3.7.2

</details>

scikit-learn

Description: Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. It strives to be simple and efficient, accessible to everybody, and reusable in various contexts. Homepage: http://scikit-learn.org/stable/index.html

Installed versions: - scikit-learn/0.20.3-foss-2019a

</details>

SciPy-bundle

Description: Bundle of Python packages for scientific software Homepage: https://python.org/

Installed versions: - SciPy-bundle/2019.03-foss-2019a - SciPy-bundle/2019.03-intel-2019a - SciPy-bundle/2019.10-foss-2019b-Python-3.7.4 - SciPy-bundle/2019.10-intel-2019b-Python-3.7.4

</details>

SCons

Description: SCons is a software construction tool. Homepage: https://www.scons.org/

Installed versions: - SCons/3.0.1-GCCcore-7.3.0-Python-2.7.15-bare - SCons/3.0.4-foss-2018b-Python-2.7.15 - SCons/3.0.5-GCCcore-8.2.0 - SCons/3.1.1-GCCcore-8.3.0

</details>

SCOTCH

Description: Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning. Homepage: http://gforge.inria.fr/projects/scotch/

Installed versions: - SCOTCH/6.0.6-foss-2018b - SCOTCH/6.0.6-gompi-2019a - SCOTCH/6.0.6-iimpi-2019a - SCOTCH/6.0.6-intel-2018b

</details>

Seaborn

Description: Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics. Homepage: http://stanford.edu/~mwaskom/software/seaborn/

Installed versions: - Seaborn/0.9.0-foss-2019a-Python-3.7.2

</details>

SeqKit

Description: SeqKit Homepage: https://github.com/shenwei356/seqkit

Installed versions: - SeqKit/0.11.0

</details>

seqtk

Description: 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. Homepage: https://github.com/lh3/seqtk/

Installed versions: - seqtk/1.3-foss-2018b

</details>

Serf

Description: The serf library is a high performance C-based HTTP client library built upon the Apache Portable Runtime (APR) library Homepage: http://serf.apache.org/

Installed versions: - Serf/1.3.9-GCCcore-7.3.0 - Serf/1.3.9-GCCcore-8.2.0

</details>

SGA

Description: Assembles large genomes from high coverage short read data. Homepage: https://omictools.com/sga-tool

Installed versions: - SGA/190808-foss-2018b-Python-3.6.6

</details>

SHAPEIT

Description: SHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data. Homepage: https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html

Installed versions: - SHAPEIT/2.r904.glibcv2.17

</details>

SHAPEIT4

Description: SHAPEIT4 is a method for estimation of haplotypes (aka phasing) for SNP array and sequencing data. Homepage: https://github.com/odelaneau/shapeit4

Installed versions: - SHAPEIT4/4.1-gompi-2019a

</details>

SLEPc

Description: 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. Homepage: http://www.grycap.upv.es/slepc/

Installed versions: - SLEPc/3.11.0-foss-2018b - SLEPc/3.11.0-intel-2018b - SLEPc/3.11.1-foss-2018b - SLEPc/3.11.1-intel-2018b

</details>

SNAP

Description: SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. SNAP is an acroynm for Semi-HMM-based Nucleic Acid Parser. Homepage: http://korflab.ucdavis.edu/software.html

Installed versions: - SNAP/2013-11-29-GCC-8.2.0-2.31.1 - SNAP/2013-11-29-GCC-8.3.0

</details>

snappy

Description: 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. Homepage: https://github.com/google/snappy

Installed versions: - snappy/1.1.7-GCCcore-8.3.0

</details>

SOAPdenovo2

Description: 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. Homepage: http://soap.genomics.org.cn/index.html

Installed versions: - SOAPdenovo2/r241-foss-2018b - SOAPdenovo2/r241-intel-2018b

</details>

SPAdes

Description: Genome assembler for single-cell and isolates data sets Homepage: http://cab.spbu.ru/software/spades/

Installed versions: - SPAdes/3.13.0-foss-2018b - SPAdes/3.13.1-GCC-8.2.0-2.31.1

</details>

sparsehash

Description: 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.

Homepage: https://github.com/sparsehash/sparsehash

Installed versions: - sparsehash/2.0.3-GCCcore-7.3.0 - sparsehash/2.0.3-GCCcore-8.2.0

</details>

Sphinx

Description: Sphinx is a tool that makes it easy to create intelligent and beautiful documentation. It was originally created for the new Python documentation, and it has excellent facilities for the documentation of Python projects, but C/C++ is already supported as well, and it is planned to add special support for other languages as well. Homepage: http://sphinx.pocoo.org/

Installed versions: - Sphinx/1.8.1-foss-2018b-Python-2.7.15

</details>

SQLite

Description: SQLite: SQL Database Engine in a C Library Homepage: https://www.sqlite.org/

Installed versions: - SQLite/3.20.1-GCCcore-7.3.0 - SQLite/3.24.0-GCCcore-7.3.0 - SQLite/3.27.2-GCCcore-8.2.0 - SQLite/3.29.0-GCCcore-8.3.0

</details>

SRA-Toolkit

Description: 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 Homepage: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software

Installed versions: - SRA-Toolkit/2.9.6-1-centos_linux64

</details>

Stacks

Description: 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.

Homepage: http://catchenlab.life.illinois.edu/stacks

Installed versions: - Stacks/1.48-intel-2018b - Stacks/2.3e-foss-2018b - Stacks/2.41-GCC-8.2.0-2.31.1 - Stacks/2.41-iccifort-2019.1.144-GCC-8.2.0-2.31.1

</details>

Stampy

Description: Stampy is a package for the mapping of short reads from illumina sequencing machines onto a reference genome Homepage: https://www.well.ox.ac.uk/research/research-groups/lunter-group/lunter-group/stampy

Installed versions: - Stampy/1.0.32-foss-2018b-Python-2.7.15

</details>

StringTie

Description: StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. Homepage: http://ccb.jhu.edu/software/%(namelower)/

Installed versions: - StringTie/1.3.5-GCCcore-8.2.0

</details>

Structure

Description: The program structure is a free software package for using multi-locus genotype data to investigate population structure. Homepage: https://web.stanford.edu/group/pritchardlab/structure.html

Installed versions: - Structure/2.3.4-GCC-7.3.0-2.30

</details>

Subversion

Description: Subversion is an open source version control system. Homepage: http://subversion.apache.org/

Installed versions: - Subversion/1.10.2-GCCcore-7.3.0 - Subversion/1.12.0-GCCcore-8.2.0

</details>

SuiteSparse

Description: SuiteSparse is a collection of libraries manipulate sparse matrices. Homepage: http://faculty.cse.tamu.edu/davis/suitesparse.html

Installed versions: - SuiteSparse/5.4.0-foss-2018b-METIS-5.1.0 - SuiteSparse/5.4.0-foss-2019a-METIS-5.1.0 - SuiteSparse/5.4.0-intel-2018b-METIS-5.1.0 - SuiteSparse/5.4.0-intel-2019a-METIS-5.1.0

</details>

Sumaclust

Description: SUMACLUST is a sequence-clustering application Homepage: https://git.metabarcoding.org/obitools/sumaclust/wikis/home

Installed versions: - Sumaclust/1.0.34-GCC-7.3.0-2.30

</details>

SUNDIALS

Description: SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers Homepage: http://computation.llnl.gov/projects/sundials

Installed versions: - SUNDIALS/2.7.0-foss-2018b

</details>

SWIG

Description: SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages. Homepage: http://www.swig.org/

Installed versions: - SWIG/3.0.12-GCCcore-8.2.0-Python-3.7.2 - SWIG/3.0.12-foss-2018b-Python-3.6.6 - SWIG/3.0.12-intel-2018b-Python-3.6.6 - SWIG/4.0.1-GCCcore-8.3.0

</details>

Szip

Description: Szip compression software, providing lossless compression of scientific data

Homepage: https://www.hdfgroup.org/doc_resource/SZIP/

Installed versions: - Szip/2.1.1-GCCcore-7.3.0 - Szip/2.1.1-GCCcore-8.2.0 - Szip/2.1.1-GCCcore-8.3.0

</details>

tabix

Description: Generic indexer for TAB-delimited genome position files Homepage: http://samtools.sourceforge.net

Installed versions: - tabix/0.2.6-GCCcore-7.3.0

</details>

tbb

Description: 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. Homepage: https://01.org/tbb/

Installed versions: - tbb/2018_U5-GCCcore-7.3.0 - tbb/2019_U4-GCCcore-8.2.0

</details>

Tcl

Description: 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.

Homepage: https://www.tcl.tk/

Installed versions: - Tcl/8.6.7-GCCcore-7.3.0 - Tcl/8.6.8-GCCcore-7.3.0 - Tcl/8.6.9-GCCcore-8.2.0 - Tcl/8.6.9-GCCcore-8.3.0

</details>

TensorFlow

Description: An open-source software library for Machine Intelligence Homepage: https://www.tensorflow.org/

Installed versions: - TensorFlow/1.13.1-fosscuda-2018b-Python-3.6.6

</details>

Theano

Description: Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently. Homepage: http://deeplearning.net/software/theano

Installed versions: - Theano/1.0.4-fosscuda-2018b-Python-3.6.6

</details>

Tigmint

Description: Tigmint identifies and corrects misassemblies using linked reads from 10x Genomics Chromium Homepage: https://github.com/bcgsc/tigmint

Installed versions: - Tigmint/1.1.2-foss-2018b-Python-3.6.6

</details>

Tk

Description: Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building a graphical user interface (GUI) in many different programming languages. Homepage: https://www.tcl.tk/

Installed versions: - Tk/8.6.8-GCCcore-7.3.0 - Tk/8.6.9-GCCcore-8.2.0 - Tk/8.6.9-GCCcore-8.3.0

</details>

Tkinter

Description: Tkinter module, built with the Python buildsystem Homepage: https://python.org/

Installed versions: - Tkinter/2.7.15-GCCcore-8.2.0 - Tkinter/2.7.15-foss-2018b-Python-2.7.15 - Tkinter/2.7.15-fosscuda-2018b-Python-2.7.15 - Tkinter/2.7.15-intel-2018b-Python-2.7.15 - Tkinter/3.6.6-foss-2018b-Python-3.6.6 - Tkinter/3.6.6-intel-2018b-Python-3.6.6 - Tkinter/3.7.2-GCCcore-8.2.0 - Tkinter/3.7.4-GCCcore-8.3.0

</details>

TotalView

Description: TotalView is a GUI-based source code defect analysis tool that gives you unprecedented control over processes and thread execution and visibility into program state and variables. It allows you to debug one or many processes and/or threads in a single window with complete control over program execution. This allows you to set breakpoints, stepping line by line through the code on a single thread, or with coordinated groups of processes or threads, and run or halt arbitrary sets of processes or threads. You can reproduce and troubleshoot difficult problems that can occur in concurrent programs that take advantage of threads, OpenMP, MPI, GPUs or coprocessors. Homepage: http://www.roguewave.com/products/totalview.aspx

Installed versions: - TotalView/2019.1.4

</details>

TransDecoder

Description: 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. Homepage: https://github.com/TransDecoder/TransDecoder/wiki

Installed versions: - TransDecoder/5.5.0-intel-2018b-Perl-5.28.0

</details>

TreeMix

Description: TreeMix is a method for inferring the patterns of population splits and mixtures in the history of a set of populations. Homepage: http://bitbucket.org/nygcresearch/treemix

Installed versions: - TreeMix/1.13-intel-2018b

</details>

TRF

Description: Tandem repeats finder: a program to analyze DNA sequences. Legacy version. Homepage: https://tandem.bu.edu/trf/trf.html

Installed versions: - TRF/4.09-linux64

</details>

Trilinos

Description: The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. A unique design feature of Trilinos is its focus on packages. Homepage: https://trilinos.org

Installed versions: - Trilinos/12.12.1-foss-2018b-Python-3.6.6 - Trilinos/12.12.1-intel-2018b-Python-3.6.6

</details>

Trim_Galore

Description: 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. Homepage: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/

Installed versions: - Trim_Galore/0.6.2-foss-2018b-Python-3.6.6

</details>

Trimmomatic

Description: 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. Homepage: http://www.usadellab.org/cms/?page=trimmomatic

Installed versions: - Trimmomatic/0.38-Java-1.8

</details>

Trinity

Description: 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. Homepage: http://trinityrnaseq.github.io

Installed versions: - Trinity/2.8.4-foss-2018b

</details>

UDUNITS

Description: UDUNITS supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of units, and conversion of values between compatible scales of measurement. Homepage: http://www.unidata.ucar.edu/software/udunits/

Installed versions: - UDUNITS/2.2.26-GCCcore-8.2.0 - UDUNITS/2.2.26-GCCcore-8.3.0 - UDUNITS/2.2.26-foss-2018b - UDUNITS/2.2.26-intel-2018b

</details>

UFL

Description: The Unified Form Language (UFL) is a domain specific language for declaration of finite element discretizations of variational forms. More precisely, it defines a flexible interface for choosing finite element spaces and defining expressions for weak forms in a notation close to mathematical notation. Homepage: https://bitbucket.org/fenics-project/ufl

Installed versions: - UFL/2018.1.0-foss-2018b-Python-3.6.6 - UFL/2019.1.0-foss-2019a-Python-3.7.2

</details>

USEARCH

Description: USEARCH is a unique sequence analysis tool which offers search and clustering algorithms that are often orders of magnitude faster than BLAST. Homepage: http://www.drive5.com/usearch/index.html

Installed versions: - USEARCH/11.0.667-i86linux32

</details>

utf8proc

Description: utf8proc is a small, clean C library that provides Unicode normalization, case-folding, and other operations for data in the UTF-8 encoding. Homepage: https://github.com/JuliaStrings/utf8proc

Installed versions: - utf8proc/2.3.0-GCCcore-8.2.0

</details>

util-linux

Description: Set of Linux utilities Homepage: https://www.kernel.org/pub/linux/utils/util-linux

Installed versions: - util-linux/2.32-GCCcore-7.3.0 - util-linux/2.33-GCCcore-8.2.0 - util-linux/2.34-GCCcore-8.3.0

</details>

Valgrind

Description: Valgrind: Debugging and profiling tools Homepage: http://valgrind.org

Installed versions: - Valgrind/3.14.0-foss-2018b - Valgrind/3.14.0-intel-2018b

</details>

VASP

Description: The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles. Homepage: http://www.vasp.at

Installed versions: - VASP/5.4.4-intel-2019a-gam - VASP/5.4.4-intel-2019a-gam-vtst - VASP/5.4.4-intel-2019a-ncl - VASP/5.4.4-intel-2019a-std - VASP/5.4.4-intel-2019a-std-vtst

</details>

VCFtools

Description: The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files. Homepage: https://vcftools.github.io

Installed versions: - VCFtools/0.1.16-foss-2018b-Perl-5.28.0 - VCFtools/0.1.16-intel-2018b-Perl-5.28.0

</details>

Velvet

Description: Sequence assembler for very short reads Homepage: http://www.ebi.ac.uk/~zerbino/velvet/

Installed versions: - Velvet/1.2.10-foss-2018b-mt-kmer_191 - Velvet/1.2.10-intel-2018b-mt-kmer_191

</details>

VISLCG3

Description: Implements the functionality of the VISL CG-2 variant of constraint grammar. Homepage: https://visl.sdu.dk/cg3.html

Installed versions: - VISLCG3/1.3.0-foss-2019a

</details>

VSEARCH

Description: 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. Homepage: https://github.com/torognes/vsearch

Installed versions: - VSEARCH/2.9.1-foss-2018b - VSEARCH/2.13.4-iccifort-2019.1.144-GCC-8.2.0-2.31.1

</details>

VTK

Description: 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. Homepage: https://www.vtk.org

Installed versions: - VTK/8.1.1-foss-2018b-Python-2.7.15 - VTK/8.1.1-foss-2018b-Python-3.6.6 - VTK/8.2.0-foss-2019a-Python-3.7.2

</details>

VTune

Description: Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java. Homepage: https://software.intel.com/en-us/vtune

Installed versions: - VTune/2019_update5

</details>

Wannier90

Description: A tool for obtaining maximally-localised Wannier functions Homepage: http://www.wannier.org

Installed versions: - Wannier90/2.1.0-intel-2019a

</details>

wheel

Description: A built-package format for Python. Homepage: https://pypi.python.org/pypi/wheel

Installed versions: - wheel/0.31.1-foss-2018b-Python-2.7.15 - wheel/0.31.1-foss-2018b-Python-3.6.6 - wheel/0.31.1-fosscuda-2018b-Python-3.6.6

</details>

X11

Description: The X Window System (X11) is a windowing system for bitmap displays Homepage: https://www.x.org

Installed versions: - X11/20180604-GCCcore-7.3.0 - X11/20190311-GCCcore-8.2.0 - X11/20190717-GCCcore-8.3.0

</details>

XML-LibXML

Description: Perl binding for libxml2 Homepage: https://metacpan.org/pod/distribution/XML-LibXML/LibXML.pod

Installed versions: - XML-LibXML/2.0132-GCCcore-7.3.0-Perl-5.28.0 - XML-LibXML/2.0200-GCCcore-8.2.0-Perl-5.28.1 - XML-LibXML/2.0201-GCCcore-8.3.0

</details>

XML-Parser

Description: This is a Perl extension interface to James Clark's XML parser, expat. Homepage: http://search.cpan.org/~toddr/XML-Parser-2.41/

Installed versions: - XML-Parser/2.44_01-GCCcore-7.3.0-Perl-5.28.0

</details>

xorg-macros

Description: X.org macros utilities. Homepage: https://cgit.freedesktop.org/xorg/util/macros

Installed versions: - xorg-macros/1.19.2-GCCcore-7.3.0 - xorg-macros/1.19.2-GCCcore-8.3.0

</details>

XZ

Description: xz: XZ utilities Homepage: https://tukaani.org/xz/

Installed versions: - XZ/5.2.4-GCCcore-7.3.0 - XZ/5.2.4-GCCcore-8.2.0 - XZ/5.2.4-GCCcore-8.3.0

</details>

YAXT

Description: Yet Another eXchange Tool Homepage: https://www.dkrz.de/redmine/projects/yaxt

Installed versions: - YAXT/0.6.0-intel-2018b - YAXT/0.6.2-iimpi-2019b

</details>

zarr

Description: Zarr is a Python package providing an implementation of compressed, chunked, N-dimensional arrays, designed for use in parallel computing. Homepage: http://zarr.readthedocs.io/en/stable/

Installed versions: - zarr/2.3.1-foss-2019a

</details>

ZeroMQ

Description: ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. It gives you sockets that carry atomic messages across various transports like in-process, inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous message-processing tasks. It has a score of language APIs and runs on most operating systems. Homepage: http://www.zeromq.org/

Installed versions: - ZeroMQ/4.2.5-foss-2018b

</details>

zlib

Description: 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.

Homepage: http://www.zlib.net/

Installed versions: - zlib/1.2.11 - zlib/1.2.11-GCCcore-6.4.0 - zlib/1.2.11-GCCcore-7.3.0 - zlib/1.2.11-GCCcore-8.2.0 - zlib/1.2.11-GCCcore-8.3.0

</details>

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