Software packages

Program URL
anaconda3 https://www.continuum.io/downloads
ansys http://www.ansys.com
cmake-3.3.1 https://cmake.org
fftw-3.3.4.gcc http://www.fftw.org
gsl-2.0 http://www.gnu.org/software/gsl
HiFiLES-solver-master https://github.com/HiFiLES/HiFiLES-solver
metis-5.1.0 http://glaros.dtc.umn.edu/gkhome/views/metis
parmetis-4.0.3 http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview
Allinea DDT http://www.allinea.com/products/ddt
Gaussian 09 http://www.gaussian.com
adf2014.08 http://www.nsccs.ac.uk/sc_adf.php
compchem http://www.compchem.net
gnuplot http://www.gnuplot.info
gromacs51 http://www.gromacs.org
molcas http://www.molcas.org
molden5.4 http://www.cmbi.ru.nl/molden/howtoget.html
NX-1.4.0-2 http://www.univie.ac.at/newtonx
vasp541 https://www.vasp.at
vmd-1.9.2 http://www.ks.uiuc.edu/Research/vmd
Octave https://www.gnu.org/software/octave
R https://www.r-project.org
Program URL
R Studio https://www.rstudio.com
Gephi https://gephi.org
cufflinks-2.2.1.Linux_x86_64 http://cole-trapnell-lab.github.io/cufflinks
FastQC http://www.bioinformatics.babraham.ac.uk/projects/fastqc
GATK-Cluster https://www.broadinstitute.org/gatk
megacc-7.0 http://www.megasoftware.net
ncbi-blast-2.3.0 http://www.ncbi.nlm.nih.gov/news/12-29-2015-blast-executables-update
vcftools_0.1.12b http://vcftools.sourceforge.net/man_0112b.html
wgsim https://github.com/lh3/wgsim
hdf 5 https://www.hdfgroup.org/HDF5
Intel composer_xe https://software.intel.com
Intel MPI https://software.intel.com
Netcdf http://www.unidata.ucar.edu/software/netcdf/docs
Freesurfer https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki
Openmpi https://www.open-mpi.org
PGI Compiler http://www.pgroup.com
BBMap http://sourceforge.net/projects/bbmap/files/BBMap_35.50.tar.gz
Bcftools http://www.htslib.org
Bedtools http://bedtools.readthedocs.org/en/latest
http://quinlanlab.org/tutorials/cshl2014/bedtools.html
Bioawk https://github.com/lh3/bioawk
BLAST ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST
Bowtie 1 and 2 http://bowtie-bio.sourceforge.net/index.shtml
http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
WGsim/DWGsim https://github.com/lh3/wgsim
https://github.com/nh13/DWGSIM
WGsim/DWGsim https://github.com/lh3/wgsim
https://github.com/nh13/DWGSIM
Cufflinks http://cole-trapnell-lab.github.io/cufflinks/
Program URL
Entrez Direct ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/edirect.zip
http://www.ncbi.nlm.nih.gov/books/NBK179288/
EMBOSS http://emboss.sourceforge.net
FlexBar http://sourceforge.net/projects/flexbar
FreeBayes https://github.com/ekg/freebayes
Kallisto pseudo-aligner https://github.com/pachterlab/kallisto/releases/download/ v0.42.4/kallisto_mac-v0.42.4.tar.gz
The LAST aligner http://last.cbrc.jp
The LASTZ aligner http://www.bx.psu.edu/~rsharris/lastz
Picard Tools http://broadinstitute.github.io/picard
PrinSeq http://prinseq.sourceforge.net
Samtools http://www.htslib.org
Seqtk https://github.com/lh3/seqtk
snpEff http://snpeff.sourceforge.net
SRA toolkit http://www.ncbi.nlm.nih.gov/Traces/sra/?view=software
Subread and FeatureCounts http://bioinf.wehi.edu.au/subread-package
Tabix http://www.htslib.org/doc/tabix.html
Tabtk https://github.com/lh3/tabtk
TopHat https://ccb.jhu.edu/software/tophat/index.shtml
Trimmomatic http://www.usadellab.org/cms/?page=trimmomatic
cdo-1.6.3 https://code.zmaw.de/projects/cdo/files
grads-2.1.a2 www.iges.org/grads
grib_api-1.13.0 https://software.ecmwf.int/wiki/display/GRIB/Home
jasper-1.900.1 https://www.ece.uvic.ca/~frodo/jasper/
libpng-1.6.16 http://www.libpng.org/pub/png/libpng.html
nco-4.4.8
wgrib2.tgz http://www.cpc.ncep.noaa.gov/products/wesley/wgrib2
zlib-1.2.8 http://www.zlib.net