name about category URL
R free software environment for statistical computing and graphics Data Analysis http://www.r-project.org
alsa Advanced Linux Sound Architecture Libraries http://alsa-project.org
amber assisted model building with energy refinement Molecular Biology http://ambermd.org
amira a powerful, multifaceted 3D software platform for visualizing, manipulating, and understanding biomedical data coming from all types of sources and modalities Graphics http://www.vsg3d.com/amira
amunmt fast neural machine translation in C++ Computer Science http://amunmt.github.io
anaconda scientific Python distribution Programming Tools http://continuum.io
anaconda3 scientific Python distribution Programming Tools http://continuum.io
ant Java Library and Command Line Tool for building packages Programming Tools http://ant.apache.org
astrobear Collection of libraries used by astrobear Libraries http://astrobear.pas.rochester.edu
atom a hackable text editor Accessories http://atom.io
bazel correct, reproducible, and fast builds for everyone Programming Tools http://github.com/bazelbuilt/bazel
beacon automated tool for Bacterial gEnome Annotation ComparisON Bioinformatics http://www.cbrc.kaust.edu.sa/BEACON
boost portable C++ source libraries Libraries http://www.boost.org
bowtie2 ultrafast memory-efficient short read aligner Bioinformatics http://bowtie-bio.sourceforge.net/bowtie2
c3d deep learning framework Computer Science http://caffe.berkeleyvision.org
caffe deep learning framework Computer Science http://caffe.berkeleyvision.org
cdf common data format Libraries https://cdf.gsfc.nasa.gov/
cmake open-source, cross-platform family of tools designed to build, test, and package software System Tools https://cmake.org
cuda CUDA software development kit Programming Tools http://developer.nvidia/com
cudnn GPU-accelerated library for deep neural networks Programming Tools http://nvidia.com
cufflinks transcript assembly, differential expression, and differential regulation for RNA-seq Bioinformatics http://cufflinks.cbcb.umd.edu
deeptools tools for exploring deep sequencing data Bioinformatics http://deeptools.readthedocs.io
digits Deep Learning GPU Training System Computer Science http://github.com/NVIDIA/DIGITS
eigen C++ template library for linear algebra Libraries http://eigen.tuxfamily.org
elmer Elmer is an open source multiphysical simulation software mainly developed by CSC - IT Center for Science (CSC) Physics http://www.csc.fi/web/elmer/elmer
fastqc quality control tool for high throughput sequence data Bioinformatics http://www.bioinformatics.babraham.ac.uk/projects/fastqc
ffmpeg cross-platform solution to record, convert, and stream audio and video Libraries http://ffmpeg.org
fftw3 FFTW3 library for computing the discrete Fourier transform (DFT) Libraries http://www.fftw.org/
firefox web browser Internet http://mozilla.org
gaussian quantum chemistry Chemistry http://www.gaussian.com
gcc GNU compiler collection Programming Tools http://gcc.gnu.org
geneious bioinformatics tools Bioinformatics http://geneious.com
gflags command line flags processing Programming Tools http://github.com/gflags
ghc Glasgow Haskell Compiler Programming Tools http://www.haskell.org
git distributed version control system Programming Tools http://git-scm.com
globus-cli A Command Line Interface to Globus Internet http://globus.org
glog google logging module Programming Tools http://github.com/glog
gnuplot portable command-line driven graphing utility Graphics http://gnuplot.info
gperf perfect hash function generator System Tools http://www.gnu.org/software/gperf/
gromacs molecular dynamics Molecular Biology http://www.gromacs.org
gstreamer library for constructing graphs of media-handling components Libraries http://gstreamer.freedesktop.org
hdf4 a library and multi-object file format for storing and managing data between machines Libraries http://www.hdfgroup.org/products/hdf4/
hdf5 data model, library, file format for storing and managing data Libraries http://www.hdfgroup.org
hdfviewer HDF file viewer System Tools http://www.hdfgroup.org/products/java/release/download.html
hypre a library for solving large, sparse linear systems of equations on massively parallel computers Libraries http://computation.llnl.gov/casc/hypre/software.html
idl scientific programming language Data Analysis http://harrisgeospatial.com
igv integrative genomics viewer Bioinformatics http://www.broadinstitute.org/igv
impi Intel MPI Programming Tools http://software.intel.com
intel Intel Parallel Studio XE Cluster Edition for Linux Programming Tools http://software.intel.com
intelpython Intel Python Programming Tools http://software.intel.com
intelpython3 Intel Python Programming Tools http://software.intel.com
jdk Java Development Kit Programming Tools http://java.com
jre Java Runtime Environment Programming Tools http://java.com
julia high-level, high-performance dynamic programming language Programming Tools http://julialang.org
jupyter Python programming language Programming Tools http://python.org
jupyterhub Python programming language Programming Tools http://python.org
kenlm estimates, filters, and language models Libraries http://kheafield.com/code/kenlm
lapack linear algebra Libraries http://www.netlib.org/lapack
leveldb lightweight single purpose library for persistence with bindings Data Analysis http://leveldb.org
libav libraries for dealing with multimedia formats Libraries http://libav.org
lmdb lightning memory-mapped database manager Programming Tools http://lmdb.tech
mathematica computation, symbolic mathematics, and visualization Mathematics http://www.wolfram.com
matlab MATLAB (matrix laboratory) is a multi-paradigm numerical computing environment and fourth-generation programming language Mathematics http://www.mathworks.com/products/matlab
meshlab open source system for processing and editing 3D triangular meshes Graphics http://meshlab.net
mgiza A word alignment tool based on famous GIZA++, extended to support multi-threading, resume training and incremental training Computer Science https://github.com/moses-smt/mgiza
molcas ab initio quantum chemistry software package Chemistry http://www.molcas.org
netcdf software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data Libraries http://www.unidata.ucar.edu/netcdf
netlogo multi-agent programmable modeling environment Programming Tools http://ccl.northwestern.edu/netlogo
nodejs Event-driven I/O server-side JavaScript environment based on V8 System Tools http://nodejs.org
openblas optimized BLAS library Libraries http://openblas.net
opencv open source computer vision library Graphics http://opencv.org
openmpi high performance message passing library Programming Tools http://openmpi.org
oracle Oracle instant client Libraries http://www.oracle.com
pandoc universal document converter Accessories http://pandoc.org
paraview an open-source, multi-platform data analysis and visualization application Graphics http://www.paraview.org/
perl Perl programming language Programming Tools http://www.perl.org
pgadmin3 PGAdmin3 Postgresql database client Programming Tools http://pgadmin.org
pgplot plotting library for fortran Libraries http://www.astro.caltech.edu/~tjp/pgplot/
protobuf protocol buffers - google data interchange format Programming Tools http://github.com/google/protobuf
pyslurm PySlurm Programming Tools https://github.com/PySlurm/pyslurm
pysox audio manipulation for python Libraries http://pythonhosted.org/pysox
python Python programming language Programming Tools http://python.org
python3 Python programming language Programming Tools http://python.org
qt cross-platform application and UI framework for developers using C++ or QML Libraries http://qt-project.org
r free software environment for statistical computing and graphics Data Analysis http://www.r-project.org
ragel executable finate state machines System Tools http://www.colm.net/open-source/ragel/
reapr evaluates the accuracy of a genome assembly using mapped paired end reads Bioinformatics http://www.sanger.ac.uk/science/tools/reapr
rmats multivariate analysis of transcript splicing Bioinformatics http://rnaseq-mats.sourceforge.net
rstudio open source and enterprise-ready professional software for R Data Analysis http://rstudio.com
samtools utilities for sequence alignment Bioinformatics http://samtools.sourceforge.net
sas data management Data Analysis http://www.sas.com
sbt build tool for Scala, Java, and more Programming Tools http://www.scala-sbt.org
scala an object-functional programming and scripting language for general software applications Programming Tools http://www.scala-lang.org
scons software construction tool Programming Tools http://www.scons.org
silo library for reading and writing a wide variety of scientific data to binary files Libraries https://wci.llnl.gov/simulation/computer-codes/silo
slurm SLURM Software System Tools http://www.schedmd.com
snappy fast compressor/decompressor System Tools http://github.com/google/snappy
sox swiss army knife of sound processing utilities Libraries http://sourceforge.net/projects/sox
spark a fast and general-purpose cluster computing system System Tools http://spark.apache.org
sparsehash extremely memory-efficient hash_map implementation Programming Tools http://code.google.com/p/sparsehash
sratoolkit access data from sequence read archive Bioinformatics http://www.ncbi.nlm.nih.gov
tensorflow computation using data flow graphs Computer Science http://tensorflow.org
texlive TeX document production system Accessories https://www.tug.org/texlive/
tmux terminal multiplexer System Tools http://tmux.github.io
tophat fast splice junction mapper for RNA-Seq reads Bioinformatics http://tophat.cbcb.umd.edi
torch scientific computing framework for luajit Programming Tools http://torch.ch
tree list contents of directories in a tree-like format System Tools http://linux.die.net/man/1/tree
vdjer B Cell Receptor Repertoire Reconstruction from short read mRNA-Seq data Bioinformatics http://github.com/mozack/vdjer
virtualgl OpenGL interposer that allows applications to use remote display hardware Libraries http://www.virtualgl.org
visit Open Source, interactive, scalable, visualization, animation and analysis tool Graphics https://wci.llnl.gov/codes/visit/
vmd visual molecular dynamics Graphics http://www.ks.uiuc.edu/Research/vmd
wxpython a blending of the wxWidgets C++ class library with the Python programming language Libraries http://wxpython.org
yaml human friendly data serialization standard for all programming languages Programming Tools http://yaml.org
zmq ZeroMQ lightweight messaging kernel Libraries http://zeromq.org