| 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 |
| nparc3r1 |
http://resource.ansys.com/staticassets/ANSYS/Initial%20Content%20Entry/General%20Articles%20-%20Products/ICEM%20CFD%20Interfaces/nparc.htm |
| 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/ |
| 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/ |
| Bedops |
http://bedops.readthedocs.org/en/latest/ |
| Bedtools |
Website:http://bedtools.readthedocs.org/en/latest/Tutorial: 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.shtmlhttp://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| WGsim/DWGsim |
Webpage: https://github.com/lh3/wgsimWebpage: https://github.com/nh13/DWGSIM |
| Cufflinks |
http://cole-trapnell-lab.github.io/cufflinks/ |
| Entrez Direct |
ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/edirect.ziphttp://www.ncbi.nlm.nih.gov/books/NBK179288/ |
| EMBOSS |
http://emboss.sourceforge.net/ |
| FastQC |
http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ |
| 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/ |