Sango Software
NOTE: This page is obsolete, and only retained for reference
This is the currently available software installed as modules on the Sango cluster. It does not currently include system-installed software or versions. Individual packages may have links to a separate page with further information and instructions. Please take a look if you intend to use it. You can browse all software usage notes on this page.
Some software comes in separate modules, with a "gpu" ending, or "gcc/icc" endings.
- "gpu" is a module built for running on the GPU nodes; they may be slow or may not run at all without a GPU available.
- "gcc" and "icc" signifies that the module (often a library) has been built with the GNU and the Intel compilers, respectively. Some code (C++ especially) can be very particular about combining code built with different compilers. You will usually want to match the library to the compiler that you use when there are multiple versions to choose from.
For general information on using the module system, see this page.
General Software
Bioinformatics
Simulation and Modelling
Software Development
Libraries
| General Software | |||
|---|---|---|---|
| Package | Version | description | |
| gnuplot | 4.4.4, 4.6.5, 5.0.2 | A portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms. | |
| jupyter.py | 2.7, 3.5 | Browser-accessible Python notebook environment for creating documents that contain live code, equations, visualizations and explanatory text. We have versions for Python 2.7 and Python 3.5. | |
| jupyter.R | 3.3.2 | Browser-accessible R and Python notebook environment for creating documents that contain live code, equations, visualizations and explanatory text. This supports R and Python 3.5. | |
| mathematica | 10.0, 8.0, 9.0 | computational software program used in many scientific, engineering, mathematical and computing fields, based on symbolic mathematics | |
| matlab | MCR, R2009b, R2011b, R2012a, R2012b, R2013a, R2013a_tah, R2013b, R2014a, R2014b, R2015a, R2015b, R2016b | high-level language and interactive environment to explore and visualize ideas in signal and image processing, communications, control systems, and computational finance | |
| mc | 4.8.14, 4.8.17 | Feature-rich full-screen text mode file manager. An internal viewer and editor are included. | |
| python | 2.7.10, 2.7.3, 2.7.8, 3.5.0, 3.5.2 | A widely used general-purpose, high-level dynamic programming language. It has extensive support for data analysis, numerical computation, graphics and system management. | |
| R | 3.0.2, 3.1.1, 3.3.2 | A popular software environment for statistical computing and graphics. | |
| Relion | 2.1 | Empirical Bayesian approach to refinement of 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM) | |
| RStudio | 1.0.143.R332 | An integrated development environment for R, the popular statistics language. | |
| scilab | 5.5.2 | Open source environment for interactive numerical computation. | |
| VisIT | 2.12.3 | A point-and-click 3D scientific visualization application that supports common visualization techniques on structured and unstructured grids. It is able to handle very large datasets interactively. | |
| vim | 8.0 | Powerful, popular programming editor. | |
| Bioinformatics | |||
|---|---|---|---|
| Package | Version | description | |
| amos | 3.1.0 | A collection of tools and class interfaces for the assembly of DNA reads. | |
| ampliconnoise | V1.27 | A collection of programs for the removal of noise from 454 sequenced PCR amplicons. | |
| augustus | 3.0.3, 3.3 | Predict genes in eukaryotic genomic sequences. | |
| bamtools | 2.3.0, 2.4.1 | Command-line toolkit for reading, writing, and manipulating BAM (genome alignment) files. | |
| bcftools | 1.3.1 | A set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. | |
| beagle | 1261, 1262, 2.1.2 | A high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. | |
| beast2 | v2.1.3, v2.4.4, v2.4.8 |
Bayesian evolutionary analysis by sampling trees. | |
| bedtools | v2.25.0 | A powerful toolset for genome arithmetic. | |
| blat.gcc | 35, 36 | Alignment tool that can quickly find sequences of 95% and greater similarity of length 25 bases or more for DNA, or sequences of 80% and greater similarity of length 20 amino acids or more for proteins. | |
| blat.icc | 35 | Alignment tool that can quickly find sequences of 95% and greater similarity of length 25 bases or more for DNA, or sequences of 80% and greater similarity of length 20 amino acids or more for proteins. | |
| bowtie | 1.1.0, 1.1.2 | Ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. | |
| bowtie2 | 2.2.3, 2.2.6 | Ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. This is version 2. | |
| BUSCO | 1.2 | Assess genome assembly and annotation completeness with benchmarking universal single-copy orthologs. | |
| bwa.gcc | 0.5.9, 0.6.1, 0.7.10 | A software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of the three algorithms BWA-backtrack, BWA-SW and BWA-MEM. | |
| bwa.icc | 0.5.9, 0.6.1, 0.7.10 | A software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of the three algorithms BWA-backtrack, BWA-SW and BWA-MEM. | |
| cdbfasta | 0.99-20100722 | Fasta file indexing and retrival tool. | |
| cd-hit |
2007-0131, 2009-0427, |
Cluster Database at High Identity with Tolerance takes a fasta format sequence database as input and produces a set of 'non-redundant' (nr) representative sequences as output. | |
| clearcut | 1.0.9 | A stand-alone reference implementation of relaxed neighbor joining (RNJ), that outputs a phylogenetic tree in Newick format and an optional corrected distance matrix. | |
| clustalw2.gcc | 2.0.12, 2.1 | Multiple alignment of nucleic acid and protein sequences. | |
| cudasw | 3.1.1 | Bioinformatics software for Smith-Waterman protein database searches that takes advantage of the massively parallel CUDA architecture of NVIDIA Tesla GPUs to perform sequence searches 10x-50x faster than NCBI BLAST. | |
| cufflinks | 2.2.1 | Transcriptome assembly and differential expression analysis for RNA-Seq. | |
| cushaw3.gcc | 3.0.3 | An open-source parallelized, sensitive and accurate short-read aligner. | |
| cushaw3.icc | 3.0.3 | An open-source parallelized, sensitive and accurate short-read aligner. | |
| exabayes | 1.5 | Bayesian tree inference package that is particularly suitable for large-scale analyses on computer clusters. | |
| examl | 3.0.17 | Exascale maximum likelihood (ExaML) code for phylogenetic inference using MPI. | |
| exonerate | 2.2.0 | A generic tool for pairwise sequence comparison. | |
| FAST | 1.06 | A set of Unix tools for sequence bioinformatics modeled after the Unix textutils, designed for inline (serial) processing of flatfile biological sequence record databases per-sequence through Unix command pipelines. | |
| fasta | 35.4.12, 36.3.7a | Search protein and DNA sequence databases, confirm the statistical significance of a match by comparing the alignment score to a distribution of scores produced by shuffled sequences. | |
| fastqc | 0.11.4, 0.11.5 | Quality-control application for high throughput sequence data. | |
| fastx_toolkit | 0.0.14 | A collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. | |
| freebayes | 0.9.10, 1.0.2 | A Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, MNPs, and complex events smaller than the length of a short-read sequencing alignment. | |
| gmap-gsnap | 2014-10-16 | Genomic mapping and alignment program for mRNA and EST Sequences (GMAP), and Genomic short-read mucleotide alignment program (SMAP). | |
| hmmer | 3.1b2 | Biosequence analysis using profile hidden Markov models. | |
| HTseq | 0.9.1 | High-throughput sequencing data analysis with Python. | |
| igv | 2.3.82 | A high-performance visualization tool for interactive exploration of large, integrated genomic datasets. | |
| infernal | 1.0.2 | A tool for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). | |
| IS_mapper | 0.1.4 | Reads paired end Illumina short read sequence data, an IS query of interest and a reference genome or assembly and reports the locations of the IS query in the reference genome or the assembly. | |
| jellyfish | 2.2.7 | Fast, memory-efficient counting of k-mers in DNA. | |
| KAT | 2.3.2 | Tools to analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts. | |
| kmergenie | 1.6950 | Estimates the best k-mer length for genome de novo assembly. | |
| last | 548 | Finds similar regions between sequences. | |
| mafft | 7.164, 7.220, 7.266, 7.305 | Multiple alignment program for amino acid or nucleotide sequences that offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc. | |
| MaSuRCA | 3.1.3 | A whole-genome assembler. | |
| MEGA | 7.0.20-1 | A sophisticated and user-friendly software suite for analyzing DNA and protein sequence data from species and populations. | |
| meraculous | 2.0.5, 2.2.2.5 | Distributed and scalable assembler for eukaryotic genomes. | |
| METAbat | 2.12.1 | A robust statistical framework for reconstructing genomes from metagenomic data. | |
| Metaxa2 | 2.1.1 | A software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets. | |
| microbiomeutil | 2010-04-29 | A set of utilities for sequence alignment (NAST-iEr) and chimera detection (ChimeraSlayer and WigeoN) from the Broad institute. | |
| Mothur | 1.25.0, 1.39.5 | Bioinformatics tool for analyzing 16S rRNA gene sequences. | |
| mpiBLAST | 1.6.0 | A parallel implementation of NCBI BLAST. | |
| MrBayes.mpi | 3.2.3 | Bayesian inference of phylogeny. | |
| mummer | 3.23 | A system for rapidly aligning entire genomes, whether in complete or draft form. | |
| muscle | 3.8.31 | A multiple alignment program with accuracy and speed that are consistently better than CLUSTALW. | |
| ncbi-blast | 2.2.22, 2.2.29+, 2.2.30+, 2.6.0+ | Find regions of local similarity between sequences. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. | |
| NextGenMap | 0.4.12 | A flexible highly sensitive short read mapping tool that handles much higher mismatch rates than comparable algorithms while still outperforming them in terms of runtime. | |
| ngsDist | 1.0.2 | Estimation of pairwise distances under a probabilistic framework. | |
| ngsF-HMM | 0.0.1b | A program to estimate per-individual inbreeding tracts using a two-state Hidden Markov Model (HMM). | |
| pagan | 20140814, 20150723 | A general-purpose method for the alignment of sequence graphs. PAGAN is based on the phylogeny-aware progressive alignment algorithm and uses graphs to describe the uncertainty in the presence of characters at certain sequence positions. | |
| pardre | 1.1.5 | A parallel tool to remove duplicate reads. Duplicate reads can be seen as identical or nearly identical sequences with some mismatches. | |
| parsinsert | 1.04 | Efficiently produces both a phylogenetic tree and taxonomic classification for sequences for microbial community sequence analysis. This is a C++ implementation of the Parsimonious Insertion algorithm. | |
| pasa | r20140417 | An eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structures, and to maintain gene structure annotation consistent with the most recently available experimental sequence data. | |
| phyldog | 2.0-git | Simultaneously build gene and species trees when gene families have undergone duplications and losses, analyzing thousands of gene families in dozens of genomes simultaneously. Trees and parameters are estimated in the maximum likelihood framework, by maximizing the probability of alignments given the species tree, the gene trees and the parameters of duplication and loss. | |
| phylobayes | 1.6j, 4.1c | Phylogenetic reconstruction using infinite mixtures. | |
| picard | 2.7.0 | A set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. | |
| platanus | 1.2.1, 1.2.4 | Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads. | |
| pplacer | v1.1 | Query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment. | |
| prank | 140603 | Tool from the Wasabi multiple sequence alignment browser. | |
| prinseq | 0.20.4 | A bioinformatics tool to PRe-process and show INformation of SEQuence data. The tool is written in Perl and can be helpful if you want to filter, reformat, or trim your sequence data. | |
| Prodigal | 2.6.2 | A microbial (bacterial and archaeal) gene finding program. | |
| pyrad | 3.0.66 | A pipeline to assemble de novo RADseq loci with the aim of optimizing coverage across phylogenetic data sets. It utilizes a wrapper around an alignment-clustering algorithm which allows for indel variation within and between samples, as well as for incomplete overlap among reads (e.g., paired-end). | |
| qiime | 1.8.0, 1.9.1 | An open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data generated on the Illumina or other platforms through to publication quality graphics and statistics. | |
| qiime2 | 2017.12 | Powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency. A complete redesign and rewrite of QIIME 1. | |
| quast | 3.1 | Quality assessment tool for genome assemblies. | |
| raxml | 7.3.0, 8.1.18, 8.2.4, 8.2.11 | A program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. It can also be used for post-analyses of sets of phylogenetic trees, analyses of alignments and, evolutionary placement of short reads. | |
| rdp_classifier | 2.2 | A naive Bayesian classifier that can rapidly and accurately provides taxonomic assignments from domain to genus, with confidence estimates for each assignment. | |
| rnammer | 1.2 | An application that predicts 5s/8s, 16s/18s, and 23s/28s ribosomal RNA in full genome sequences. | |
| RSEM | 1.3.0 | Estimate gene and isoform expression levels from RNA-Seq data. | |
| rtax | 0.984 | Rapid and accurate taxonomic classification of short paired-end sequence reads from the 16S ribosomal RNA gene. | |
| samtools | 0.1.19, 1.0, 1.2, 1.3.1 | Various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. | |
| seqmonk | 1.38.1 | A tool to visualise and analyse high throughput mapped sequence data. | |
| snpeff | 4.3g | A genetic variant annotation and effect prediction toolbox. It annotates and predicts the effects of variants on genes (such as amino acid changes). | |
| SOAPdenovo | r241 | Novel short-read assembly method that can build a de novo draft assembly for human-sized genomes, and is specially designed to assemble Illumina GA short reads | |
| sourcetracker | 0.9.5 | Bayesian approach to estimating the proportion of a novel community that comes from a set of source environments. | |
| SPAdes | 3.6.2 | An assembly toolkit containing various assembly pipelines, intended for both standard isolates and single-cell MDA bacteria assemblies. | |
| sra-tools | 2.8.2 | Tools to access the INSDC SRA (Sequence Read Archives). | |
| sspace | 3.0 | Stand-alone program for scaffolding pre-assembled contigs using NGS paired-read data. | |
| stacks | 1.34, 1.42, 1.47 |
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 | |
| tax2tree | v1.0 | A tool for automatically decorating taxonomy onto a phylogenetic tree. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. | |
| telseq | 0.0.1.20160817 | Estimate telomere length from whole genome sequencing data. | |
| tmhmm | 2.0c | Prediction of transmembrane helices in proteins. | |
| tophat | 2.1.1 | A fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, then analyzes the mapping results to identify splice junctions between exons. | |
| tpp | 5.0.0 | A completely free software solution for MS/MS-based shotgun proteomics analysis. | |
| Trimmomatic | 0.33 | A flexible trimmer for Illumina sequence data. | |
| Trinity | 2.1.1, 2.3.2 | Assemble transcript sequences from Illumina RNA-Seq data. | |
| Trinotate | 3.1.1 | A comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. | |
| uclust | 1.2.22q | High-speed sequence clustering, alignment and database search. | |
| ucsc_utils | 9999 | Tools and utilities created by the UCSC Genome Bioinformatics Group. | |
| usearch | 5.2.236, 8.0.1616 | High-throughput search and clustering. | |
| varscan | 2.4.3 | A platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments. | |
| vsearch | 1.8.0, 2.4.3 | A high-throughput tool for 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. | |
| Simulation and Modelling | |||
|---|---|---|---|
| Package | Version | description | |
| abinit | 8.2.3 | Find the total energy, charge density and electronic structure of systems made of electrons and nuclei within Density Functional Theory (DFT), using pseudopotentials (or PAW atomic data) and a planewave basis. | |
| bertini | 1.5.1 | Software for numerical algebraic geometry, specifically for numerical solutions of systems of ploynomial equtions. | |
| caffe | 1.0, rc3 | A deep learning framework made with expression, speed, and modularity in mind. | |
| caffe2 | 0.7 | A deep learning framework made with expression, speed, and modularity in mind. | |
| caffe2.gpu | 0.7 | A deep learning framework made with expression, speed, and modularity in mind. | |
| caffe.gpu | 1.0, rc3 | A deep learning framework made with expression, speed, and modularity in mind. | |
| ccp4 | 6.5 | Software for macromolecular X-ray crystallography. | |
| comsol | 43a, 43b, 44, 50, 51, 52 | software to model and simulate any physics-based system | |
| crystalwave | 4.9 | Computing engine for the CAD environment for the layout, design and optimisation of integrated optics components, which has been optimised for the modelling of photonic crystals structures (2D and 3D lattices) | |
| csds | 2016.0 | The Cambridge Structural Database System | |
| dials | 1.3.5, 452 | Diffraction integration for advanced light sources. | |
| Gaussian | 09RE01 | Gaussian series of programs for electronic structure modeling | |
| lammps | 15May15, 6Mar15 | A large-scale parallel atomic/molecular dynamics simulator. | |
| MaterialsStudio | 2016 | Solve key materials and chemical research problems with an integrated, multi-scale modeling environment that delivers a complete range of simulation methods. | |
| MOLGEN | 50 | Molecular structure generator of the molecular graphs that correspond to a given chemical formula and prescribed and forbidden substructures. | |
| motioncorr | 2.1 | This program corrects whole frame image motion recorded with dose fractionated image stack. | |
| NAMD | 2.12 | Parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. | |
| neuron | 7.3 | Empirically-based simulations of neurons and networks of neurons. | |
| nwchem | 6.6 | An ab initio computational chemistry software package which also includes quantum chemical and molecular dynamics functionality. | |
| OpenFOAM | 4.1 | An open-source CFD software package. | |
| phenix | 1.9-1692, dev-1951, 1.12-2829 |
Python-based hierarchical environment for integrated crystallography. | |
| QE | 6.0 | An integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials. | |
| siesta | 4.0 | Perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. | |
| XMDS | 2.2.3 | Fast and easy solution of sets of ordinary, partial and stochastic differential equations, using a variety of efficient numerical algorithms. | |
| Software Development | |||
|---|---|---|---|
| Package | Version | description | |
| allinea | 5.1, 6.0 | C, C++ and Fortran 90 debugger and profiler | |
| autotools | 1.15 | The GNU configuration and building toolchain. This module includes Make, M4, Autoconf, Automake, Autogen, Libtool and pkg-config. | |
| binutils | 2.24, 2.25, 2.27 | A collection of development-related utilities, including assembler and linker, profiler and tools to manipulate Linux object files. | |
| cmake | 3.2.1, 3.3.1, 3.6.0, 3.6.2 | Extensible, open-source build system that manages the build process in an operating system and compiler-independent manner. | |
| cpptest | 1.1.2 | A portable and powerful, yet simple, unit testing framework for handling automated tests in C++. The focus lies on usability and extendability. | |
| cuda | 5.5.22, 6.0.37, 6.5.14, 7.0.28, 7.5.18, 8.0.27 | A software system and API that lets you use NVIDIA GPUs to accellerate general numerical computing tasks using C, C++ or Fortran. | |
| gcc | 4.7.4, 4.9.2, 6.2.0 | The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, Ada, and Go, as well as libraries for these languages. | |
| gdb | 7.11.1 | A full-featured source debugger with support for local and remote debugging for a large number of languages and systems. | |
| ghc | 6.8.3 | Glasgow Haskell Compiler; open source compiler and interactive environment for the functional language Haskell | |
| git | 2.3.2 | A popular open-source distributed version control system that works well with both small and large projects. | |
| glog | 0.3.3 | C++ implementation of the Google logging module. | |
| hwloc | 1.10.1, 1.6.1 | A portable abstraction of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores, network interfaces, InfiniBand HCAs and GPUs. | |
| intel | 2013_sp1_update3, 2015_update2, 2015_update3, 2015_update6, 2016_update2, 2016_update4, 2017 | Intel® Parallel Studio XE tool suite simplifies the design, development, debug, and tuning of code that utilizes parallel processing to boost application performance | |
| intel.mpi | 2015_update3, 2015_update6, 2016_update2, 2016_update4, 2017, 4.1.1.036, 5.0.3.048 | Intel MPI compiler | |
| intel.mpirt | 2013_sp1_update3, 2015_update2 | Intel MPI runtime application and libraries | |
| java-jdk | 1.6.0_45, 1.7.0_67, 1.8.0_20 | A general-purpose computer programming language that is concurrent, class-based, object-oriented and portable across a wide range of systems. | |
| julia | 0.3.8, 0.4.0, 0.4.6, 0.5.0, 0.6.0 |
A high-level, high-performance dynamic programming language for technical computing. It provides a sophisticated compiler, distributed parallel execution, numerical accuracy, and an extensive mathematical function library. | |
| mpe2.gcc | 1.3.0, 2.4.9b | Useful tools for MPI programs. | |
| neon | 0.30.0 | A HTTP and WebDAV client with a C interface. | |
| ruse | 1.0 | Measure the time and memory your program needs when run as a Slurm job. | |
| valgrind | 3.10.1, 3.11.0, 3.9.0 | An instrumentation framework for building dynamic analysis tools that can automatically detect many memory management and threading bugs, and profile your programs in detail. | |
| vcftools | 0.1.12b | A package for working with VCF files, such as those generated by the 1000 Genomes Project. | |
| Libraries | |||
|---|---|---|---|
| Package | Version | description | |
| argtable | 2.13 | Argtable is an ANSI C library for parsing GNU style command line options with a minimum of fuss. | |
| arpack | 3.1.5, 3.4.0 | A collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. | |
| ATLAS | 3.10.2 | A library that provides C and Fortran77 interfaces to a portably efficient BLAS implementation, as well as a few routines from LAPACK. | |
| boost | 1.55.0, 1.57.0, 1.59.0, 1.61.0 | A set of free peer-reviewed portable C++ source libraries. | |
| boost.intel | 1.57.0, 1.61.0 | A set of peer-reviewed portable C++ source libraries (Intel compiler version). | |
| cuDNN | 2.0_CUDA_6.5, 4.0_CUDA_7.0.58, 5.0_CUDA_7.5.18, 5.1_CUDA_7.5.18, 5.1_CUDA_8.0.27, 6.0a_CUDA_7.5.18, 6.0_CUDA_7.5.18, 6.0_CUDA_8.0.27 | GPU-accelerated library of primitives for deep neural networks. | |
| gdata | 2.0.17 | The Google Data APIs (Google Data) provide a simple protocol for reading and writing data on the web. This library provides helpful tools to streamline your code and keep up with server-side changes. | |
| glib | 2.31.20 | Core application building blocks for libraries and applications written in C. | |
| eigen | 3.3.1 | A versatile, fast C++ template library for linear algebra; matrices, vectors, numerical solvers, and related algorithms. | |
| fftw.gcc | 3.3.4, 3.3.5 | Fast, popular Fast Fourier transform library. | |
| fftw.icc | 3.3.4, 3.3.5 | Fast, popular Fast Fourier transform library. | |
| hdf5.gcc | 1.8.14, 1.8.15, 1.8.16, 1.8.17 | 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. | |
| hdf5.icc | 1.8.14, 1.8.15, 1.8.16, 1.8.17 | 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. | |
| glpk | 4.54 | An ANSI C library for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems. | |
| gsl | 1.16, 2.0 | An open-source 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. | |
| libav | 11.7 | Audio and video transcoding library and commandline tools. | |
| opencl.intel | 1.2-4.5.0.8 | OpenCL library for the Intel Phi accellerator. Deprecated. | |
| opencv | 2.4.11, 3.2.0 | Comprehensive open-source computer vision library. | |
| opencv.gpu | 2.4.11 | Comprehensive open-source computer vision library. | |
| openmpi.gcc | 1.10.1, 1.10.3a1(default), 1.6.5, 1.7.5, 1.8.6, 1.8.7, 1.8.8 | A high performance message passing library. This is the system installed version. | |
| openmpi.icc | 1.7.5, 1.8.6, 1.8.7, 1.8.8 | A high performance message passing library. | |
| uriparser | 0.8.0.1, 0.8.4 | URI parsing and handling library written in C. Cross-platform, fast, supports Unicode and is licensed under the New BSD license. | |
| SuiteSparse | 4.4.2, 4.4.4, 4.5.5 | A suite of sparse matrix algorithms, including UMFPACK, CHOLMOD, SPQR, KLU, BTF, CSparse, CXSparse, UFget, spqr_rank, Factorize, SSMULT, SFMULT. | |
| vcflib | 1.0.0-rc1 | A simple C++ library for parsing and manipulating VCF files, with many command-line utilities. | |
| voro++.gcc | 0.4.6 | A software library for carrying out three-dimensional computations of the Voronoi tessellation. It is particularly well-suited for applications that rely on cell-based statistics, where features of Voronoi cells (eg. volume, centroid, number of faces) can be used to analyze a system of particles. | |
| voro++.icc | 0.4.6 | A software library for carrying out three-dimensional computations of the Voronoi tessellation. It is particularly well-suited for applications that rely on cell-based statistics, where features of Voronoi cells (eg. volume, centroid, number of faces) can be used to analyze a system of particles. | |
| zlib | 1.2.8 | A general library for lossless data compression. | |