Scientific Software Guide

Package Research Area Webpage Details
AMBER Biology, Chemistry, Material Science, Physics http://ambermd.org/ view
Anaconda view
Armadillo Biology, Computer Science, Health Science, Mathematics, Statistics, Linux Library http://arma.sourceforge.net/ view
BamTools Biology, Linux Utility https://github.com/pezmaster31/bamtools/wiki view
bazel view
BCFtools Linux Utility http://www.htslib.org/doc/bcftools-1.0.html view
Beast Biology http://beast.community/ view
BLAST+ Biology http://www.ncbi.nlm.nih.gov/books/NBK1763/ view
Boost Biology, Linux Library http://www.boost.org/ view
Bowtie 2 Biology http://bowtie-bio.sourceforge.net/index.shtml view
BWA Biology http://bio-bwa.sourceforge.net/ view
Bzip2 Biology http://www.bzip.org/ view
Cairo Biology https://cairographics.org/ view
CD-Hit Biology http://weizhongli-lab.org/cd-hit/ view
CMAKE Linux Utility http://www.cmake.org/ view
Cufflinks Biology view
Curl Biology https://curl.haxx.se/ view
dDocent Biology https://ddocent.wordpress.com/about/ view
DL_POLY Chemistry http://www.stfc.ac.uk/cse/25526.aspx view
Ea-Utils Biology https://expressionanalysis.github.io/ea-utils/ view
Eigen Biology http://eigen.tuxfamily.org/index.php view
Espresso Material Science http://www.quantum-espresso.org/ view
FastxToolkit Biology http://hannonlab.cshl.edu/fastx_toolkit/ view
FFTW Linux Library http://www.fftw.org/ view
GAMESS Chemistry http://www.msg.chem.iastate.edu/gamess/index.html view
Gatk Biology https://software.broadinstitute.org/gatk/ view
Gaussian Chemistry view
glibc Biology https://www.gnu.org/software/libc/ view
GNU Plot Linux Library http://www.gnuplot.info/ view
Go view
Gromacs Biology, Chemistry http://www.gromacs.org/ view
GSL Biology https://www.gnu.org/software/gsl/ view
Gulp Biology https://github.com/gulpjs/gulp view
hadoop view
HDF5 Linux Library https://www.hdfgroup.org/HDF5/ view
Hisat Biology https://ccb.jhu.edu/software/hisat/index.shtml view
HTSlib Biology https://github.com/samtools/htslib view
ICU Biology http://site.icu-project.org/ view
Intel Linux Utility, Linux Library https://software.intel.com/en-us/intel-parallel-studio-xe view
JAGS Education, Statistics http://mcmc-jags.sourceforge.net/ view
Java Computer Science https://go.java/index.html view
Kallisto Biology https://pachterlab.github.io/kallisto/ view
Keras Computer Science https://keras.io/ view
Kraken Biology https://ccb.jhu.edu/software/kraken/ view
LAMMPS Chemistry, Material Science http://lammps.sandia.gov/ view
Lapack Biology http://www.netlib.org/lapack/ view
Libtool Biology https://www.gnu.org/software/libtool/ view
MATHEMATICA Mathematics, Statistics http://www.wolfram.com/mathematica/ view
MATLAB Mathematics, Statistics http://www.mathworks.com/index.html view
Minimac2 Biology https://www.ncbi.nlm.nih.gov/pubmed/25338720 view
Mpiblast Biology http://www.mpiblast.org/ view
Namd Biology http://www.ks.uiuc.edu/Research/namd/ view
Ncurses Linux Utility https://invisible-island.net/ncurses/announce.html view
NWChem Chemistry http://www.nwchem-sw.org/index.php/Main_Page view
Oases Biology http://www.ebi.ac.uk/~zerbino/oases/ view
Openblas Biology http://www.openblas.net/ view
Opencv Computer Science https://opencv.org/ view
Openfoam view
OpenMPI Linux Library https://www.open-mpi.org/ view
Ovito Chemistry, Computer Science https://ovito.org/ view
Paraview Linux Utility https://www.paraview.org/ view
Perl Linux Utility https://www.perl.org/ view
Picard Computer Science https://broadinstitute.github.io/picard/ view
Plink Biology http://zzz.bwh.harvard.edu/plink/ view
PSI4 Chemistry http://www.psicode.org/ view
Pssh Linux Utility https://linux.die.net/man/1/pssh view
pyMPI Biology http://pympi.sourceforge.net/ view
Python Linux Utility https://www.python.org/ view
R Education view
RAxML Biology http://sco.h-its.org/exelixis/web/software/raxml/ view
Readline Linux Utility https://tiswww.case.edu/php/chet/readline/rltop.html view
SageMath Mathematics http://www.sagemath.org/ view
SAMTOOLS Biology http://samtools.sourceforge.net/ view
seqprep Biology https://github.com/jstjohn/SeqPrep view
SKLearn Linux Utility http://scikit-learn.org/stable/index.html view
SOAPdenovo Biology http://soap.genomics.org.cn/soapdenovo.html view
Spades Linux Utility https://secure.hosting.vt.edu/www.arc.vt.edu/userguide/spades/ view
Spark view
Stacks Biology view
Star Computer Science http://star.mit.edu/ view
Stringtie Biology https://ccb.jhu.edu/software/stringtie/ view
Szip Biology https://support.hdfgroup.org/doc_resource/SZIP/ view
Tensorflow Computer Science https://www.tensorflow.org/ view
TopHat Biology http://ccb.jhu.edu/software/tophat/index.shtml view
Trinity Biology https://github.com/trinityrnaseq/trinityrnaseq/wiki view
VASP Chemistry view
Velvet Biology http://www.ebi.ac.uk/~zerbino/velvet/ view
Visit Computer Science https://wci.llnl.gov/simulation/computer-codes/visit/ view
VMD Biology http://www.ks.uiuc.edu/Research/vmd/ view
WARP Physics https://sites.google.com/a/lbl.gov/warp/home view
Zlib Linux Utility https://zlib.net/ view