| Program | Version | Link to main page |
|---|
| bamtools | 2.5.1 | pezmaster31/bamtools: C++ API & command-line toolkit for working with BAM data |
| augustus | 3.3.2 | Augustus: gene prediction |
| cmake | 3.7.2
3.13.2 | CMake - Cross Platform Make |
| RHash | 1.3.7 | rhash/RHash: Great utility for computing hash sums |
| FFTW | 3.3.6
3.3.7 | FFTW Home Page |
| GCC | 5.4.0
6.3.0
7.3.0
8.3.0 | GCC, the GNU Compiler Collection - GNU Project - Free Software Foundation (FSF) |
| GMP | 6.1.2 | The GNU MP Bignum Library |
| grib_api | 1.19.0 | Home - GRIB-API - ECMWF Confluence Wiki |
| GSL | 2.2.3 | GSL - GNU Scientific Library - GNU Project - Free Software Foundation (FSF) |
| Gurobi Optimizer | 5.6.3
7.0.2
8.1.0
9.0.0 | Gurobi Optimizer |
| HDF5 | 1.8.18 | HDF Group - HDF5 |
Intel Parallel Studio- Intel compilers
- MKL
- DAAL
- IPP
- TBB
| 2017.1
2017.4 | Intel® Composer XE Suites |
| Intel-MKL | 2019.3.199 | Intel® Math Kernel Library (Intel® MKL) | Intel® Software |
| matlab | R2016b
2018a | MATLAB - The Language of Technical Computing |
| MPC | 1.0.3 | MPC |
| MPFR | 3.1.5 | The GNU MPFR Library |
| NCO | 4.6.4 | NCO Homepage |
| netcdf | 4.4.1.1 | Unidata | NetCDF |
| netcdf-cxx | 4.3.0 | Unidata | NetCDF |
| netcdf-fortran | 4.4.4 | Unidata | NetCDF |
openmpi | 2.0.1
2.1.2 | Open MPI: Open Source High Performance Computing |
| Python | | Welcome to Python.org |
| R | | The R Project for Statistical Computing |
| valgrind | 3.12.0 | Valgrind Home |
| ocaml | 4.04.0 | OCaml |
| Ansys | 17.2 | ANSYS - Simulation Driven Product Development |
| CFITSIO | 3.410 | FITSIO Home Page |
| Pythia | 8.223 | PYTHIA |
| Platypus | 0.8.1 | Platypus Variant Caller |
| Ruby | 2.4.0 | Ruby Programming Language |
| Julia | 0.5.0
0.5.1 | The Julia Language |
| MOSEK | 8.0.0.53
8.0.0.80 | MOSEK ApS |
| JDK | 8u121
8u172 | Java SE | Oracle Technology Network | Oracle |
| RSL | 1.49 | RSL (Radar Software Library) |
| Perl | 5.24.1 | The Perl Programming Language |
| Postgresql | 11.2 | PostgreSQL: The world's most advanced open source database |
| Graphviz | 2.40.1 | Graphviz - Graph Visualization Software |
| htslib | 1.3.2 | Releases · samtools/htslib |
| samtools | 1.3.1 | Releases · samtools/samtools |
| bcftools | 1.3.1 | Releases · samtools/bcftools |
| bedtools | 2.26.0 | bedtools: a powerful toolset for genome arithmetic |
| lzo | 2.09 | LZO real-time data compression library |
| CUDA | 8.0.44
8.0.61
9.0.176.1
9.1.85.1
9.1.85.2 | Parallel Programming and Computing Platform | CUDA | NVIDIA |
| Beagle-lib | 2.1.2
3.1.2 | general purpose library for evaluating the likelihood of sequence evolution on trees |
| Tecplot360 | 2016R2 | Tecplot 360 CFD post processing tools to analyze data |
| CDO | 1.8.0 | Overview - CDO |
| I/O API | 3.2 | CMAS: Community Modeling and Analysis System I/O API |
| Plink | 1.07 | PLINK: Whole genome data analysis toolset |
| CMAQ | 5.1 | Community Multi-scale Air Quality (CMAQ) Modeling System for Air Quality Management | Air Research | US EPA |
| NCL | 6.4.0 | NCL Overview |
| HDF-EOS2 | 2.19 | HDF-EOS Tools and Information Center |
| HDF-EOS5 | 1.15 | HDF-EOS Tools and Information Center |
| g2clib | 1.60 | GRIB2 |
| Gaussian 09 | D.01 | Gaussian.com | Expanding the limits of computational chemistry |
| NBO | 6.0 | NATURAL BOND ORBITAL 6.0 HOME |
| HDF | 4.2.1 | HDF Group - HDF4 |
| AutoDock Vina | 1.1.2 | AutoDock Vina - molecular docking and virtual screening program |
| BEAST | 1.8.4 | BEAST Software - Bayesian Evolutionary Analysis Sampling Trees |
| XCrySDen | 1.5.60 | XCrySDen - (X-Window) Crystalline Structures and Densities |
| Mesa | 17.0.1 | The Mesa 3D Graphics Library |
| LLVM | 4.0.0 | The LLVM Compiler Infrastructure Project |
| Open Babel | 2.4.1 | Open Babel |
| Eigen | 3.3.3 | Eigen |
| Protobuf (C++) | 3.2.0 | Protocol Buffers | Google Developers |
| Snappy | 1.1.4 | Snappy by google |
| LevelDB | 1.20 | GitHub - google/leveldb: LevelDB is a fast key-value storage library written at Google that provides an ordered mapping from string keys to string values. |
| YASM | 1.3.0 | The Yasm Modular Assembler Project |
| FFMPEG | 3.2.4 | About FFmpeg |
| OpenCV | 3.2.0 | OpenCV library |
| JAGS | 4.2.0 | JAGS - Just Another Gibbs Sampler |
| STAR-CCM+ | 12.02.010
13.04.010 | STAR-CCM+® | CFD Simulation Software |
| Cufflinks | 2.2.1 | Cufflinks |
PETSc- hpre
- metis
- parmetis
- mpi4py
- mumps
- petsc4py
- ptscotch
- suitesparse
- superlu_dist
| 3.7.5
3.10.3 | PETSc: Home Page |
| Wannier90 | 2.1.0 | wannier.org |
| Atompaw | 4.0.0.14 | Atompaw Web Page |
| Libxc | 2.2.3
3.0.0 | Libxc - OctopusWiki |
| ABINIT | 8.2.2 | ABINIT |
| c-blosc | 1.11.2 | Blosc, an extremely fast, multi-threaded, meta-compressor library | Blosc Main Page |
| MDTraj | 1.8.0 | MDTraj |
| lmfit | 6.1 | lmfit [MLZ Scientific Computing Group] |
| Gromacs | 2016.3 | Gromacs |
| ELPA | 2016.05.004
2018.11.001 | About ELPA — Eigenvalue SoLvers for Petaflop-Applications (ELPA) |
| Quantum Espresso | 6.1 | Quantum ESPRESSO |
| BWA | 0.7.15 | Burrows-Wheeler Aligner |
| libcerf | 1.5 | libcerf [MLZ Scientific Computing Group] |
| Gnuplot | 5.0.6 | gnuplot homepage |
| GEOS | 3.6.1 | GEOS |
| Ncview | 2.1.7 | Ncview |
| git | 2.13.0 | Git |
BLAST
databases: nt, nt, swissprot | 2.6.0+ | BLAST: Basic Local Alignment Search Tool |
| ParaView | 5.4.0 | ParaView Home |
| cuDNN | 5.1
6.0
7.0.5 | NVIDIA cuDNN | NVIDIA Developer |
| Leptonica | 1.74.4 | Leptonica |
| Tesseract | 3.05.01 | Tesseract Open Source OCR Engine |
| WebP | 0.6.0 | A new image format for the Web | WebP | Google Developers |
| giflib | 5.1.4 | The GIFLIB project |
| Subread | 1.5.2 | Subread |
| GLPK | 4.62 | GLPK - GNU Project - Free Software Foundation (FSF) |
| Symphony | 5.6.16 | SYMPHONY |
| gavl | 1.4.0 | Gmerlin homepage - gavl |
| frei0r-plugins | 1.6.1 | Frei0r :: Free Video Effects collection |
| MPFI | 1.5.1 | InriaForge: MPFI: Project Home |
| ESBTL | 1.0-beta01 | ESBTL (Easy Structural Biology Template Library) |
| gf2x | 1.2 | InriaForge: gf2x: Project Home |
| NTL | 10.4.0 | NTL: A Library for doing Number Theory |
| CGAL | 4.10
4.13 | The Computational Geometry Algorithms Library |
| SQLite | 3.16.2
3.30.0 | SQLite Home Page |
| scotch | 6.0.4 | SCOTCH: Static Mapping, Graph, Mesh and Hypergraph Partitioning, and Parallel and Sequential Sparse Matrix Ordering Package |
| metis | 5.1.0 | METIS - Serial Graph Partitioning and Fill-reducing Matrix Ordering | Karypis Lab |
| parmetis | 4.0.3 | ParMETIS - Parallel Graph Partitioning and Fill-reducing Matrix Ordering | Karypis Lab |
| OpenFOAM | 4.1
5.0 | OpenFOAM | Free CFD Software | The OpenFOAM Foundation |
| STAR | 2.5.3a | STAR | Spliced Transcripts Alignment to a Reference |
| libunwind | 1.2.1 | The libunwind project |
| glog | 0.3.5 | google/glog: C++ implementation of the Google logging module |
| gflags | 2.2.1 | How To Use Gflags (formerly Google Commandline Flags) |
| LMDB | 0.9.21 | LMDB/lmdb: Read-only mirror of official repo on openldap.org. |
| Caffe | 1.0 | Caffe | Deep Learning Framework |
| NCCL | 1.3.4
2.1.4 | NVIDIA/nccl: Optimized primitives for collective multi-GPU communication |
| 17.1 | WIEN 2k |
| Turbomole | 7.2.0 7.2.1 | Turbomole: Program Package for ab initio Electronic Structure Calculations |
| Parallel NetCDF | 1.8.1 | parallel-netcdf |
| Amber | 2017 (Amber16 + AmberTools17) | The Amber Molecular Dynamics Package |
| TransPS | 1.1.0 | TransPS |
| cusplibrary | 0.4.0
0.5.1 | CUSP: Main Page |
| Mesquite | 2.3.0 | Mesquite – The Trilinos Project |
| foam-extend | 4.0 | foam-extend download | SourceForge.net |
| HPL | 2.2 | HPL - A Portable Implementation of the High-Performance Linpack Benchmark for Distributed-Memory Computers |
| PortAudio | 19.6.0 | PortAudio - an Open-Source Cross-Platform Audio API |
| openSMILE | 2.3.0 | audEERING | Intelligent Audio Engineering – openSMILE |
| log4j | 2.10.0 | Log4j – Apache Log4j 2 - Apache Log4j 2 |
| flex | 2.6.4 | GitHub - westes/flex: The Fast Lexical Analyzer - scanner generator for lexing in C and C++ |
WRF
WRF-chem
WPS (WRF Preprocessing System) | 3.9.1.1 | Weather Research and Forecasting Model | MMM: Mesoscale & Microscale Meteorology Laboratory |
| Darshan | 3.5.1 | Darshan |
| RngStreams | 1.0.1 | RngStreams - multiple independent streams of pseudo-random numbers |
| UNU.RAN | 1.8.1 | UNU.RAN - Universal Non-Uniform RANdom number generators |
| LZ4 | 1.8.1.2 | LZ4 - Extremely fast compression |
| GL2PS | 1.4.0 | GL2PS: an OpenGL to PostScript printing library |
| XRootD | 4.8.1 | Home Page | XRootD |
| Z3 | 4.6.0 | GitHub - Z3Prover/z3: The Z3 Theorem Prover |
| Davix | 0.6.7 | GitHub - cern-it-sdc-id/davix: High-performance file management over WebDAV / HTTP |
| xxHash | 0.6.4 | GitHub - Cyan4973/xxHash |
| Oracle instantclient | 12.2.0.1.0 | Oracle Instant Client - Free tools and libraries for connecting to Oracle Database |
| ROOT | 6.12.06 | ROOT a Data analysis Framework |
| Praat | 6.0.37 | Praat: doing Phonetics by Computer |
| MKL-DNN | 0.12 | GitHub - intel/mkl-dnn: Intel(R) Math Kernel Library for Deep Neural Networks (Intel(R) MKL-DNN) |
| NASM | 2.13.03 | NASM |
| Yeppp | 1.0.0 | MDukhan / Yeppp — Bitbucket |
| CNVnator | 0.3.3 | GitHub - abyzovlab/CNVnator: a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads |
| CPLEX | 12.8.0 | ILOG CPLEX Optimization Studio | IBM |
| 9.4_TS1M2 | Foundation Tools | SAS |
| Gentle | 0.10.1 | lowerquality/gentle: gentle forced aligner |
| Bazel | 0.12.0 | Bazel - a fast, scalable, multi-language and extensible build system - Bazel |
| TensorBoard | 1.7.0 | tensorflow/tensorboard: TensorFlow's Visualization Toolkit |
| TensorFlow | 1.7.0 | TensorFlow |
| libedit | 3.1-20170329 | Editline Library (libedit) - Port of NetBSD Command Line Editor Library |
| GEANT4 | 10.4.1 | Overview | geant4.web.cern.ch |
| Google Test | 1.8.0 | google/googletest: Google Test |
| InsightToolkit | 4.13.0
4.13.2 | ITK - Segmentation & Registration Toolkit |
| RTK | 1.4.0 | RTK - Reconstruction Toolkit |
| Gate | 8.1 | Forewords | GATE |
| SimplElastix | 0.10.0 | SimpleElastix |
| Elastix | 4.9.0 | elastix |
| PGI Community Edition | 18.4 | PGI | Products | Community Edition |
| Nettle | 3.4 | Nettle - a low-level crypto library |
| libarchive | 3.3.2 | libarchive - C library and command-line tools for reading and writing tar, cpio, zip, ISO, and other archive formats |
| SRA-tools | 2.9.0 | ncbi/sra-tools: SRA Tools |
| NGS | 2.9.0 | ncbi/ngs: NGS Language Bindings |
| NCBI-VDB | 2.9.0-1 | ncbi/ncbi-vdb: ncbi-vdb |
| LASzip | 2.2.0
3.2.2 | LASzip - free and lossless LiDAR compression |
| libLAS | 1.8.1 | libLAS - LAS 1.0/1.1/1.2 ASPRS LiDAR data translation toolset — liblas.org |
| libgeotiff | 1.4.2 | GeoTIFF |
| libgpuarray | 0.7.6 | Welcome to libgpuarray’s documentation! |
| GATK | 4.0.5.2 | GATK | Home |
| SNAP | 0.15 | SNAP Sequence Aligner |
| zstd | 1.3.5 | Zstandard - Real-time data compression algorithm |
| magma | 2.4.0 | Magma |
| ZeroMQ | 4.2.5 | Distributed Messaging |
| CUB | 1.8.0 | CUB: Main Page |
| pybind11 | 2.2.3 | pybind/pybind11: Seamless operability between C++11 and Python |
| pytorch/caffe2 | 0.4.0 | PyTorch |
| torchvision | 0.2.1 | pytorch/vision: Datasets, Transforms and Models specific to Computer Vision |
| bowtie | 1.2.2 | Bowtie: An ultrafast, memory-efficient short read aligner |
| bowtie2 | 2.3.4.2 | Bowtie 2: fast and sensitive read alignment |
| WRF-Hydro | 5.0.0 | Overview | NCAR Research Applications Laboratory | RAL |
| libuuid | 1.0.3 | libuuid download | SourceForge.net |
| CZMQ | 4.1.1 | CZMQ - High-level C Binding for ZeroMQ - libzapi |
| cppzmq | 4.3.0 | zeromq/cppzmq: Header-only C++ binding for libzmq |
| libtool | 2.4.6 | GNU Libtool - GNU Project - Free Software Foundation |
| libunistring | 0.9.10 | libunistring - GNU Project - Free Software Foundation (FSF) |
| libatomic_ops | 7.6.4 | ivmai/libatomic_ops: The atomic_ops project (Atomic memory update operations portable implementation) |
| GC | 7.6.4 | A garbage collector for C and C++ |
| Guile | 2.2.4 | GNU's programming and extension language — GNU Guile |
| libctl | 4.1.3 | Overview - libctl Documentation |
| OpenBUGS | 3.2.3 | FrontPage - OpenBUGS |
| TopHat | 2.1.1
2.1.2 | TopHat |
| VCFtools | 0.1.16 | VCFtools |
| Jellyfish | 2.2.10 | gmarcais/Jellyfish: A fast multi-threaded k-mer counter |
| BLAT | 35 | Human BLAT Search |
| Mapsembler2 | 2.2.4 | mapsembler2 |
| cortex_con | 0.04c (beta) | CORTEX website (cortex_con) |
| cortex_var | 1.0.5.21 | CORTEX website (cortex_var) |
| CoNIFER | 0.2.2 | Conifer - COpy Number Inference From Exome Reads - Home |
| libgtextutils | 0.7 | agordon/libgtextutils: Gordon's Text utils Library |
| fastx_toolkit | 0.0.14 | agordon/fastx_toolkit: FASTA/FASTQ pre-processing programs |
| 2018 | Abaqus Unified FEA - SIMULIA™ by Dassault Systèmes® |
| GMT | 5.4.4 | GenericMappingTools/gmt: The Generic Mapping Tools |
| RocksDB | 5.17.2 | RocksDB | A persistent key-value store | RocksDB |
| TeXLive | 20180414 | TeX Live - TeX Users Group |
| ARPACK-NG | 3.7.0 | opencollab/arpack-ng: Collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. |
| SuperLU | 5.2.1 | SuperLU: Home Page |
| Armadillo | 9.200.7 | Armadillo: C++ library for linear algebra & scientific computing |
| PEST | 13.6 | PESThomePage.org - HOME PAGE |
| FEniCS | 2018.1.0 | FEniCS Project |
| mpiP | 3.4.1 | mpiP: Lightweight, Scalable MPI Profiling |
| PAPI | 5.7.0 | PAPI |
| SimpleITK | 1.2.0 | SimpleITK |
| OpenJDK | 11.0.2 | OpenJDK |
| libogg | 1.3.3 | Xiph.org |
| flac | 1.3.2 | FLAC - Free Lossless Audio Codec |
| mpg123 | 1.25.10 | mpg123, Fast MP3 Player for Linux and UNIX systems |
| libvorbis | 1.3.6 | Xiph.org |
| libsndfile | 1.0.28 | Libsndfile |
| lame | 3.100 | LAME MP3 Encoder |
| libmad | 0.15.1b | Underbit: MAD (MPEG Audio Decoder) |
| libid3tag | 0.15.1b | Underbit: MAD (MPEG Audio Decoder) |
| opus | 1.3.1 | Opus Codec |
| wavpack | 5.1.0 | WavPack Audio Compression |
| TwoLAME | 0.3.13 | TwoLAME - MPEG Audio Layer 2 Encoder |
| libao | 1.2.0 | Xiph.org: libao: a cross platform audio library |
| opencore-amr | 0.1.5 | opencore-amr download | SourceForge.net |
| opusfile | 0.11 | Opus Codec |
| SoX | 14.4.2 | http://sox.sourceforge.net/ |
| SCons | 3.0.5 | SCons: A software construction tool - SCons |
| ISCE2 | 2.3.1 | isce-framework/isce2: InSAR Scientific Computing Environment version 2 |
| Mono | 5.18.0.240 | Home | Mono |
| VASP | 5.4.4 | VASP - Vienna Ab initio Simulation Package |
| zip | 3.0 | Info-ZIP Home Page |