Installed Software

Below you will find a list of software that's available on our resources via our module system. These are loaded with the "module load DESIRED_MODULE/VERSION" command. Depending on which cluster you're logged in to you will have access to different modules/software packages. List available modules with "module avail". More information about UPPMAX module system.

Notice: Before you can load any bioinformatics software, you will have to issue the command "module load bioinfo-tools".

If you are having trouble loading one of several build-related tools, including autoconf, automake, m4, sparsehash, and cmake, you may need to issue the command "module load build-tools".

UPPMAX buys, supports and updates software for scientific computing of general interest for researchers. The software is mainly made available on UPPMAX computer systems, but also on other computer systems within Uppsala University, when license agreements allows it. Examples of software are compilers (C, C++, F90) and software for electronic structure calculations, GAUSSIAN and GAMESS-US.

For information on how to use and write MPI and OpenMP parallel programs on Milou and Rackham, see the tutorial.

For support, please email support@uppmax.uu.se.

List of Software

Software Module Cluster Version License
Compilers and build tools
Allinea DDT ddt Rackham, Irma, Bianca, Snowy 7.0 Commercial
Ant ant Rackham, Irma, Bianca, Snowy 1.9.8, 1.10.0 Apache 2.0
autoconf autoconf Rackham, Irma, Bianca, Snowy 2.69 GPL
automake automake Rackham, Irma, Bianca, Snowy 1.14.1, 1.16.1 GPL
Gnu binutils binutils Rackham, Irma, Bianca, Snowy 2.26, 2.28, 2.30 GPL v2, v3; LGPL v2, v3
gcc gcc Rackham, Irma, Bianca, Snowy 4.x, 5.x, 6.x, 7.x, 8.x, 9.x gpl
Git git Rackham, Irma, Bianca, Snowy 2.5.0, 2.10.2, 2.16.1, 2.21.0 LGPL 2.1
Guile guile Rackham, Irma, Bianca, Snowy 1.8.8 LGPL 2.1
intel intel Rackham, Irma, Bianca, Snowy 15.x, 16.x, 17.x, 18.x site license, 2 users
Java JDK java Rackham, Irma, Bianca, Snowy sun_jdk1.6.0_04, sun_jdk1.6.0_18, sun_jdk1.7.0_25, sun_jdk1.8.0_40, 

sun_jdk1.8.0_92, sun_jdk1.8.0_151

Other
Julia julia Rackham, Irma, Bianca, Snowy 1.1.1 MIT
libtool libtool Rackham, Irma, Bianca, Snowy 2.4.6 GPL
m4 m4( load build-tools module for access) Rackham, Irma, Bianca, Snowy 1.4.17 GPL
Maven maven Rackham, Irma, Bianca, Snowy 3.6.0 Apache 2.0
Meson meson Rackham, Irma, Bianca, Snowy 0.49.2 Apache 2.0
Mono mono Rackham, Irma, Bianca, Snowy 3.12.0, 5.8.1.0, 5.10.1.27 Custom open source
Ninja ninja Rackham, Irma, Bianca, Snowy 1.9.0 Apache 2.0
patchelf patchelf Rackham, Irma, Bianca, Snowy 0.8 GPL v3
Perl perl Rackham, Irma, Bianca, Snowy 5.18.2, 5.18.4, 5.22.2, 5.24.0, 5.24.1, 5.26.2 (5.24+ build with 64-bit ints and pointers) GPL, Perl
Perl Modules/Packages (large collection) perl_modules Rackham, Irma, Bianca, Snowy 5.18.4, 5.24.1, 5.26.2 GPL, Perl
Perl 6 perl6 Rackham, Irma, Bianca, Snowy rakudo-star-2017.04, rakudo-star-2019.03 Artistic License 2.0
pgi pgi Rackham, Snowy 16.x, 17.x, 18.x, 2017, 2018 site license, 5 users
Python python Rackham, Irma, Bianca, Snowy 2.7.6, 2.7.9, 2.7.11, 2.7.15, 3.3, 3.3.1, 3.4.3, 3.5.0, 3.6.0, 3.6.8, 3.7.2 GPL
Python 3 (does not conflict with python module) python3 Rackham, Irma, Bianca, Snowy 3.6.0, 3.6.8, 3.7.2 GPL
Ruby ruby Rackham, Irma, Bianca, Snowy 2.4.1, 2.5.0, 2.6.2 Ruby license
Subversion subversion Rackham, Irma, Bianca, Snowy 1.9.3 Apache 2.0
Chemistry/Physics
DOCK DOCK Rackham, Irma, Bianca, Snowy 3.7 Free Academic License
Gaussian
 
g03
g09
Milou, Tintin
g03.d02, g03.e01, g09.a02, g09.c01, g09.d01
UU site license
turbomole turbo Rackham, Irma, Bianca, Snowy 7.3 proprietary group license
TmoleX TmoleX Rackham, Irma, Bianca, Snowy 18 proprietary group license
gamess gamess Milou 20110811R1 20101001R1 20070324R1 academic site license
VASP vasp Milou, Rackham 4.6.34, 5.2.8, 5.2.11, 5.2.12, 5.4.1 user group license
molcas molcas Milou 7.8.082, 8.0.15-03-08 user group license

gromacs

gromacs Milou, Rackham 4.5.5, 4.6.3, 4.6.5, 5.0.4, 5.1.1 gpl

desmond

desmond Milou 2.2, 2.4, 2.4.2.1 gpl
nonmem nonmem Milou 7.1.0, 7.1.2, 7.2.0, 7.3.0
MOLDEN molden Rackham 5.1
Engineering
Matlab matlab Milou, Rackham 7.4, 7.8, 7.10, 7.13, 8.0, 8.1, R2014a, R2015a, R2015b, R2016a site license
envi envi Milou 4.8
openfoam openfoam Rackham 2.4.0, v1612+
Comsol comsol Rackham, Milou 4.4, 5.2a UU site license
Geospatial
CDO CDO Rackham, Irma, Bianca, Snowy 1.9.7.1, 1.9.7.1-intel18.3 GPL v2
ecCodes ecCodes Rackham, Irma, Bianca, Snowy 2.13.1
GDAL GDAL Rackham, Irma, Bianca, Snowy 2.1.0 X/MIT style Open Source
GEOS GEOS Rackham, Irma, Bianca, Snowy 3.5.0 LGPL
libgeotiff libgeotiff Rackham, Irma, Bianca, Snowy 1.4.1, 1.4.3 X-style and custom open-source "as is"
Magics Magics Rackham, Irma, Bianca, Snowy 3.3.1, 3.3.1-intel18.3 Apache 2.0
OpenFYBA / SOSI FYBA Rackham, Irma, Bianca, Snowy 4.1.1 Custom open-source "as is"
PROJ.4 PROJ.4 Rackham, Irma, Bianca, Snowy 4.9.2, 4.9.3, 4.9.3-intel18.3 MIT
Statistics
JAGS JAGS Rackham, Irma, Bianca 4.2.0, 4.3.0 GPL v2
R R Rackham, Irma, Bianca, Snowy 3.0.2, 3.2.2, 3.2.3, 3.3.0, 3.3.1, 3.3.2, 3.4.0, 3.4.3, 3.5.0, 3.5.2, 3.6.0, 3.6.1 GPL
R packages. Starting with 3.5.0, includes most packages available on CRAN and Bioconductor R_packages Rackham, Irma, Bianca, Snowy 3.3.0, 3.3.1, 3.3.2, 3.4.0, 3.4.3, 3.5.0, 3.5.2, 3.6.0, 3.6.1
RStudio RStudio Rackham, Irma, Bianca, Snowy 1.0.136, 1.0.143, 1.0.153, 1.1.423, 1.1.463 AGPL
stata stata Milou 12
Misc Applications
agrep agrep Rackham, Irma, Bianca, Snowy 3.41.5 ISC Open Source
albacore albacore Rackham, Irma, Bianca, Snowy build-4aee41d GPL3
Amazon Web Services Command Line Interface awscli Rackham, Irma, Bianca, Snowy 1.11.140, 1.16.225 Apache 2.0
BlobTools blobtools Rackham, Irma, Bianca, Snowy 1.0, 1.1.1 GPL v3
Circos circos Rackham, Irma, Bianca, Snowy 0.69-9 GPL v3
CMake cmake Rackham, Irma, Bianca, Snowy 3.5.1, 3.7.2, 3.13.2 BSD 3-Clause
Cowsay cowsay Rackham, Irma, Bianca, Snowy 3.03 Artistic License
Doxygen doxygen Rackham, Irma, Bianca, Snowy 1.8.11 Gnu GPL 2
eLSA eLSA Rackham, Irma, Bianca, Snowy eLSA/20160907-febe2d7a57c8
GNU Emacs emacs Rackham, Irma, Bianca, Snowy 25.2 GPL v3
Gnu awk gawk Rackham, Irma, Bianca, Snowy 4.1.4 GPL v3
Gnuplot gnuplot Rackham, Irma, Bianca, Snowy 5.0.7, 5.2.7 Custom open-source "as-is"
groff groff Rackham, Irma, Bianca, Snowy 1.22.3 GPL
h5utils h5utils Milou, Rackham, Irma, Bianca 1.12.1 GPL v2+
Haskell Tool Stack haskell-stack Milou, Rackham, Irma, Bianca 1.0.4.3, 1.4.0 Custom "as is"
ImageMagick ImageMagick Milou, Rackham, Irma, Bianca 6.9.9-35 Apache 2.0
MariaDB MariaDB Milou, Rackham, Irma, Bianca 10.1.29, 10.2.11 GPL v2
mbuffer mbuffer Milou, Rackham, Irma, Bianca 20151002 GPL v3
MCL mcl Milou, Rackham, Irma, Bianca 14-137 GPL v3
p7zip p7zip Rackham, Irma, Bianca, Snowy 16.02 LGPLv2
PostgreSQL PostgreSQL Milou, Rackham, Irma, Bianca 10.3 PostgreSQL Licence
POV-Ray povray Rackham, Irma, Bianca 3.7 AGPL v3
ROOT ROOT Milou, Rackham, Irma, Bianca 6.04.08, 6.06.08 LGPL v2.1
rvtests rvtests Rackham, Irma, Bianca 2.0.6
SCons SCons Milou, Rackham, Irma, Bianca 2.5.0 misc free software
SWIG swig Milou, Rackham, Irma, Bianca 3.0.7 GPL v3 plus some "as is"
SQLite sqlite Milou, Rackham, Irma, Bianca (system), 3.8.5, 3.11.1, 3.16.2 Public domain
Texinfo texinfo Milou, Rackham, Irma, Bianca 6.0 GPL v3
TeX Live texlive Milou, Rackham, Irma, Bianca 2015, 2016 misc free software
tinyutils tinyutils Milou, Rackham, Irma, Bianca 1.1, 1.2, 1.3, 1.4 GPLv2
tmux tmux Milou 1.9a
XZ Utils xz Milou, Rackham, Irma, Bianca 5.2.2 Mixed
VIM vim Rackham, Irma, Bianca, Snowy 7.4-1941, 8.0-16, 8.0-1360, 8.1-1053 Custom
Parallel
mpjexpress mpjexpress Milou 0.38
intelmpi intelmpi Milou, Irma, Rackham 5.1.2, 5.1.3, 17.0, 17.1, 17.2
openmpi openmpi Milou, Irma, Rackham 1.4, 1.4.4, 1.45, 1.5, 1.5.5, 1.6, 1.6.3, 1.6.4, 1.7, 1.7.0, 1.7.1, 1.10.0, 1.10.1, 1.10.2, 2.0.1, 2.0.2 GPL
GNU parallel gnuparallel Rackham, Irma, Bianca, Snowy 20170122, 20180822 GPL
Libraries
Armadillo Armadillo Milou, Rackham, Irma, Bianca 20170510 Apache License 2.0
ATLAS ATLAS Milou, Rackham, Irma, Bianca 3.10.3 BSD-style
BLAS and CBLAS blas Milou, Rackham, Irma, Bianca 3.6.0 Open source
Boost boost Rackham, Irma, Bianca, Snowy 1.55.0_gcc4.8.3, 1.59.0_gcc4.9.2, 1.61.0_gcc5.3.0, 1.63.0_gcc6.3.0, 1.63.0_gcc6.3.0_mpi2.0.2, 1.70.0_gcc9.1.0, 1.70.0_gcc9.1.0_mpi3.1.3, 1.70.0_intel18.3, 1.70.0_intel18.3_mpi3.1.3 Boost licence
bzip2 bzip2 Milou, Rackham, Irma, Bianca 1.0.6 Custom open source "as is"
Cairo cairo Rackham, Irma, Bianca, Snowy 1.14.8, 1.14.12, 1.17.2 GNU LGPL v2.1 or Mozilla Public Licence 1.1
fftw fftw Milou 2.1.5, 3.2.2
FreeType freetype Milou, Rackham, Irma, Bianca 2.6, 2.7.1 BSD-like FreeType and GPL v2
GIFLIB giflib Milou, Rackham, Irma, Bianca 5.1.4 Custom "as is"
GLPK glpk Rackham, Irma, Bianca, Snowy 4.63, 4.65 GPL
Gnu Scientific Library gsl Milou, Rackham, Irma, Bianca 1.16, 2.1, 2.3 GPL
HDF4 hdf4 Milou, Rackham, Irma, Bianca 4.2.11_gcc4.9.2 BSD-style open source
HDF5 hdf5 Rackham, Irma, Bianca, Snowy 1.8.18, 1.8.18_gcc6.3.0, 1.10.5, 1.10.5-intel18.3 BSD-style open source
jemalloc jemalloc Rackham, Irma, Bianca, Snowy 3.6.0, 5.0.1 BSD-derived
libcurl libcurl Rackham, Irma, Bianca, Snowy 7.45.0 Custom open source "as is"
libHaru libharu Rackham, Irma, Bianca, Snowy 2.3.0 ZLIB/LIBPNG License
NetCDF netcdf Rackham, Irma, Bianca, Snowy 4.7.1, 4.7.1-intel18.3 Custom open source "as is"
OpenBLAS openblas Rackham, Irma, Bianca, Snowy 0.2.14a, 0.2.19, 0.2.19-singlethread BSD 3-clause
PCRE pcre Rackham, Irma, Bianca, Snowy 8.40 BSD 3-clause
Poppler Poppler Rackham, Irma, Bianca, Snowy 0.54.0, 0.75.0 GPL v2
scalapack scalapack Milou 1.8.0
sparsehash sparsehash Milou, Rackham, Irma, Bianca 2.0.2, 2.0.3
SZIP szip Milou, Rackham, Irma, Bianca 2.1_gcc4.9.2, 2.1.1 BSD-style open source
Intel Threading Building Blocks tbb Milou 4.4u1_gcc4.9.2, 4.4u1_intel15.3 GPL v2
UDUNITS UDUNITS Rackham, Irma, Bianca 2.2.26 Custom open source "as is"
Yeppp Yeppp Milou, Rackham, Irma, Bianca 1.0.0 Custom open source "as is"
zlib zlib Milou, Rackham, Irma, Bianca 1.2.8, 1.2.11 ZLIB License
Bioinformatics Alignment Module Cluster Version License
AGE AGE Milou, Rackham, Irma, Bianca 0.4
ANFO anfo Milou, Rackham, Irma, Bianca 0.98 GPL
ARAGORN aragorn Milou, Rackham, Irma, Bianca 1.2.36, 1.2.38
Barrnap barrnap Milou, Rackham, Irma, Bianca 0.2, 0.6, 0.8
Blasr and associated utilities blasr Rackham, Irma, Bianca, Snowy 20150922, 5.3-20161121-e901e48, 5.3-20171117-f72428d, 5.3.2 Open source redistributable "as is"
BLAST (legacy) blast Milou, Rackham, Irma, Bianca 2.2.15, 2.2.18, 2.2.22, 2.2.23, 2.2.24, 2.2.25, 2.2.26 Public Domain
BLAST blast Milou, Rackham, Irma, Bianca 2.2.23+, 2.2.24+, 2.2.25+, 2.2.27+, 2.2.28+, 2.2.29+, 2.2.31+, 2.4.0+, 2.5.0+, 2.6.0+, 2.7.1+ Public Domain
BLAT blat Rackham, Irma, Bianca, Snowy 34, 35, 36 Open-source and strictly non-commercial
BWA bwa Rackham, Irma, Bianca, Snowy 0.5.8a, 0.5.9, 0.6.1, 0.6.2, 0.7.4, 0.7.8, 0.7.10, 0.7.12, 0.7.13, 0.7.15, 0.7.17 GPL
bwa.kit bwakit Milou, Rackham, Irma, Bianca 0.7.12 GPL
ClustalO clustalo Milou, Rackham, Irma, Bianca 1.2, 1.2.4
ClustalW clustalw Milou, Rackham, Irma, Bianca 2.1 LGPL
DIAMOND  diamond Rackham, Irma, Bianca, Snowy 0.7.9, 0.7.12, 0.8.26, 0.9.10, 0.9.24 Other open-source
Exonerate exonerate Rackham, Irma, Bianca, Snowy 2.2.0, 2.4.0 GPL v3
FASTA fasta Rackham, Irma, Bianca, Snowy 36.3.6d, 36.3.6f, 36.3.8, 36.3.8h Apache 2.0
GEM-Tools GEM-Tools Rackham, Irma, Bianca, Snowy 1.7.1 GPL (GEM-Tools) and custom non-commercial (GEM library)
GeneID geneid Milou, Rackham, Irma, Bianca 1.4.4 GPL
GMAP-GSNAP gmap-gsnap Rackham, Irma, Bianca, Snowy 2014-01-21, 2015-09-28, 2016-05-01, 2017-09-11, 2018-02-12, 2018-07-04 Custom as-is
HAL hal Milou, Rackham 20151218, 20161130 open-source "as is" and others
HISAT2 HISAT2 Rackham, Irma, Bianca, Snowy 2.1.0 GPL
HMMER hmmer Milou, Rackham, Irma, Bianca 2.3.2-gcc, 2.3.2-intel, 3.0, 3.1b1, 3.1b2, 3.1b2-intel (MPI support, compiled with intel/17.2 and openmpi/2.1.0) GPL
Infernal infernal Milou, Rackham, Irma, Bianca 1.1.1, 1.1.2 BSD
LAST last Milou, Rackham, Irma, Bianca 847 GPL v3
LASTZ lastz Milou, Rackham, Irma, Bianca 1.03.54, 1.04.00
LEON-BIS LEON-BIS Milou, Rackham, Irma, Bianca 20130322
MAFFT MAFFT Milou, Rackham, Irma, Bianca 7.205, 7.245, 7.310, 7.407 BSD (main), mixed open-source (extensions)
MafFilter MafFilter Milou, Rackham, Irma, Bianca 1.1.2
mafTools mafTools Milou 20141112 "As is" open source
Maq maq Milou, Rackham, Irma, Bianca 0.7.1 GPL
MinCED minced Milou, Rackham, Irma, Bianca 0.2.0 GPL v3
Minimap2 minimap2 Rackham, Irma, Bianca, Snowy 2.4, 2.14, 2.16 MIT
MOSAIK mosaik-aligner Milou, Rackham, Irma, Bianca 1.0.1388, 1.1.0021, 2.2.3, 2.2.26, 2.2.30 GPL
MPIBlast mpiblast Milou 1.6.0 GPL
Multiz multiz Milou, Rackham, Irma, Bianca 012109
MUMmer MUMmer Rackham, Irma, Bianca, Snowy 3.22, 3.23, 3.9.4alpha, 4.0.0beta2 Artistic License 2
MUSCLE muscle Milou, Rackham, Irma, Bianca 3.8.31, 3.8.1551 Public domain
Nextflow Nextflow Milou, Rackham, Irma, Bianca 0.17.3, 0.22.2, 0.26.0 GPLv3
NextGenMap NextGenMap Milou, Rackham, Irma, Bianca 0.4.12, 0.5.4 Artistic License 1.0
OMBlast OMBlast Milou, Rackham, Irma, Bianca 1.0 unknown
OPTIMA optima Milou, Rackham, Irma, Bianca f-1.3 GPL v2
pblat pblat Milou, Rackham, Irma, Bianca 1.6, 2.0 Same as blat
pblat-cluster pblat-cluster Milou, Rackham, Irma, Bianca 0.1, 0.3 Same as blat
pfam_scan pfam_scan Milou, Rackham, Irma, Bianca 1.3, 1.5, 1.6 GPL v3
pplacer pplacer Milou, Rackham, Irma, Bianca 1.1.alpha19 GPL v3
PRANK prank Milou, Rackham, Irma, Bianca 150803, 170427 (not milou) GPL v2+
ProbCons ProbCons Milou, Rackham, Irma, Bianca 1.12 Public domain
progressiveCactus progressiveCactus Milou 2015-02-06, 2015-12-18, 2016-11-30 GPL v3, mostly
QualiMap QualiMap Milou, Rackham, Irma, Bianca 2.0.2, 2.2 GPL
RNAmmer rnammer Milou, Rackham, Irma, Bianca 1.2
SiBELia SiBELia Rackham, Irma, Bianca, Snowy 3.0.6, 3.0.7
SortMeRNA (original site) SortMeRNA Rackham, Irma, Bianca, Snowy 2.0, 2.1b, 3.0.3 GPL v3
Spaln spaln Milou, Rackham, Irma, Bianca 2.3.1 GPL v2
SplitSeek splitseek Milou 1.3.2, 1.3.3, 1.3.4 GPL
Stampy Stampy Rackham, Irma, Bianca, Snowy 1.0.27, 1.0.32 Custom (non-commercial)
STAR star Rackham, Irma, Bianca, Snowy

2.3.1o, 2.5.1b, 2.5.2b, 2.5.3a, 2.7.0e, 2.7.0f, 2.7.1a, 2.7.2b

MIT, GPLv3 (prior to 2.7.2b)
T-Coffee T-Coffee Milou, Rackham, Irma, Bianca 11.00.8cbe486 GPL v2
TRF trf Milou 4.07b
tRNAscan-SE tRNAscan-SE Milou, Rackham, Irma, Bianca 1.3.1 GPL
Vmatch Vmatch Milou, Rackham, Irma, Bianca 2.2.5, 2.3.0 Custom non-commercial
Vsearch vsearch Milou, Rackham, Irma, Bianca 2.3.2, 2.4.3, 2.5.2 Dual GPL/BSD
Wise2 wise2 Milou, Rackham, Irma, Bianca 2.2.0, 2.4.1 Other
Bioinformatics Annotation Module Cluster Version License
AAT AAT Rackham, Irma, Bianca, Snowy r03052011 Custom "AS IS"
Augustus augustus Rackham, Irma, Bianca, Snowy 3.2.2, 3.2.3, 3.2.3_Perl5.24.1 Artistic License
CEGMA cegma Rackham, Irma, Bianca, Snowy 2.5
Delly delly Rackham, Irma, Bianca, Snowy 0.7.6, 0.7.7 GPL v3
EggNOG mapper and EggNOG databases 4.5.1 eggNOG-mapper Rackham, Irma, Bianca, Snowy 1.0.3 GPL v2
GEMINI GEMINI Rackham, Irma, Bianca, Snowy 0.18.3, 0.19.0, 0.20.0, 0.20.1 MIT
GenomeThreader GenomeThreader Rackham, Irma, Bianca, Snowy 1.7.0 Custom "AS IS"
HaMStR HaMStR Rackham, Irma, Bianca, Snowy 13.2.3 GNU GPL 3
InterProScan InterProScan Rackham, Irma, Bianca, Snowy 5.30-69.0 Misc
MAKER maker Rackham, Irma, Bianca, Snowy 2.31.9, 3.01.1-beta, 3.01.2-beta, 3.01.2-beta-mpi GPL
Oncotator oncotator Rackham, Irma, Bianca, Snowy 1.9.9.0 BROAD INSTITUTE SOFTWARE LICENSE AGREEMENT FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
Phobius Phobius Rackham, Irma, Bianca, Snowy 1.01 Private study, education and non-profit research only
Scipio Scipio Rackham, Irma, Bianca, Snowy 1.4.1 Custom non-commercial
SignalP SignalP Rackham, Irma, Bianca, Snowy 4.1c, 4.1f Custom academic user licence
sissrs sissrs Rackham, Irma, Bianca, Snowy 1.4 Open source
snpEff snpEff Rackham, Irma, Bianca, Snowy 4.1, 4.2, 4.3t LGPL
STAR-Fusion together with Genome Resource Libraries star-fusion Rackham, Irma, Bianca, Snowy 1.0.0, 1.2.0, 1.5.0, 1.7.0 Broad Institute redistributable as-is
TMHMM tmhmm Rackham, Irma, Bianca, Snowy 2.0c Custom academic as-is
TransDecoder TransDecoder Rackham, Irma, Bianca, Snowy 2.0.1, 5.0.1, 5.3.0 Broad Institute redistributable as-is
Trinotate trinotate Rackham, Irma, Bianca, Snowy 3.0.2, 3.1.1
Bioinformatics Assembly Module Cluster Version License
A5-MiSeq A5-miseq Milou, Rackham 20140113, 20140604, 20160825 GPL
ABySS abyss Milou, Rackham, Irma, Bianca 1.2.3, 1.2.4, 1.2.5, 1.2.7 1.2.7-maxk96, 1.3.0, 1.3.2, 1.3.3, 1.3.3-k96, 1.3.4, 1.3.5, 1.3.5-max, 1.3.7, 1.3.7-max, 1.3.7-k128, 1.5.2, 1.9.0, 1.9.0-k128, 2.0.2, 2.0.2-k128 GPL v3
AllPathsLG allpathslg Milou, Irma 47300, 49618, 52485
AMOS AMOS Milou, Rackham, Irma, Bianca 3.0.0, 3.1.0 Artistic
ARC assembler ARC_assembler Milou 1.1.3 Apache 2.0
BESST BESST Milou 1.0.4.3, 1.0.4.4
CABOG (WGA assembler, Celera Assembler), includes PBcR cabog, CA (synonym) Milou, Rackham, Irma, Bianca 8.1, 8.3 GPL v2 and others for subcomponents
Canu canu Rackham, Irma, Bianca, Snowy 1.5, 1.6, 1.7, 1.7-86da76b, 1.8 GPL v2 and others for subcomponents
DBG2OLC DBG2OLC Milou 20151208
DISCOVAR de novo DISCOVARdenovo Milou 51885 Custom "as is"
FALCON FALCON Milou 0.3.0, 0.4.1 Custom "as is"
FALCON-integrate FALCON-integrate Milou 20161113 Custom "as is"
fermi fermi Milou, Rackham, Irma, Bianca 1.1-r751-beta
Flye Flye Rackham, Irma, Bianca, Snowy 2.3.5, 2.4.2 BSD 3-clause
GAEMR gaemr Milou, Rackham, Irma, Bianca 1.0.1
GARM GARM Rackham, Irma, Bianca 0.7.3
IDBA IDBA Milou 1.1.1 (max read length 128 bp), 1.1.1-384 (max 384 bp) GPL 2
Kourami kourami Rackham, Irma, Bianca, Snowy 0.9.6 BSD 3
LoRDEC LoRDEC Rackham, Irma, Bianca, Snowy 0.9 CeCILL 2.1
MaSuRCA MaSuRCA Milou, Rackham, Irma, Bianca 2.0.3.1, 2.1.0, 2.3.2, 3.1.3, 3.2.1, 3.2.2, 3.2.3
MEGAHIT megahit Milou, Rackham, Irma, Bianca 1.0.3, 1.1.2 GPL v3
MetAMOS MetAMOS Milou 1.5rc3 GPLv2 and other open source
Metassembler Metassembler Milou 1.5 open-source
MHAP MHAP Milou 1.6 Apache 2.0
Miniasm miniasm Milou 20160128 MIT
Minimap minimap Milou, Rackham, Irma, Bianca 20160114 MIT
MIRA mira Milou 3.0.0, 3.2.0, 3.4.0.1, 4.0.0rc4, 4.0.2 GPL
Oases oases Milou 0.2.08 GPL
PBSuite (contains PBJelly and PBHoney) PBSuite Milou, Rackham, Irma, Bianca 15.8.24 Custom redistributable "as is"
Pilon Pilon Milou, Rackham, Irma, Bianca 1.17, 1.22 GPL v2
Platanus Platanus Rackham, Irma, Bianca, Snowy 1.2.1, 1.2.4 GPL v3
Platanus-allee Platanus-allee Rackham, Irma, Bianca, Snowy 2.0.2 GPL v3
RACA (Reference-Assisted Chromosome Assembly) RACA Milou 0.9.1.1
Ragout Ragout Milou, Rackham, Irma, Bianca 2.0-20170312 GPL v3.0
Ray Ray Milou, Rackham, Irma, Bianca 0.0.4, 0.0.7, 1.6.1, 2.3.0, 2.3.1, 2.3.1-mpiio (with support for MPI I/O, but this seems not to work very well) GPL
REAPR REAPR Milou, Rackham, Irma, Bianca 1.0.17, 1.0.18 GPL
Redundans Redundans Rackham, Irma, Bianca, Snowy 0.13a-20170321, 0.14a-de_novo-42e8edf-20190314 (development only), 0.14a-d11d32b-20190313 GPL v2
satsuma2 satsuma2 Milou, Rackham, Irma, Bianca 2016-12-07 LGPL v3+
SGA SGA Rackham, Irma, Bianca, Snowy 0.10.14 GPL v3
SMARTdenovo SMARTdenovo Rackham, Irma, Bianca, Snowy 20180219-5cc1356 Misc open source
SOAPcorrector SOAPcorrector Rackham, Irma, Bianca, Snowy 1.0
SOAPdenovo soapdenovo Milou, Rackham, Irma, Bianca 1.05, 2.04-r240
SOAPdenovo-Trans soapdenovo-trans Milou, Rackham, Irma, Bianca 1.03, 1.04 GPL v3
SPAdes spades Rackham, Irma, Bianca, Snowy 3.6.0, 3.8.0, 3.8.1, 3.9.0, 3.10.0, 3.10.1, 3.11.1, 3.12.0, 3.13.1 GPL v3
StringTie StringTie Milou, Rackham, Irma 1.2.0, 1.3.3 Artistic
Tigmint tigmint Rackham, Irma, Bianca, Snowy 1.1.2 GPL v3
Trans-ABySS transabyss Milou 1.5.3 BCCA "As Is"
Trinity trinity Milou, Rackham, Irma, Bianca 2011-05-13, 2011-10-29, 2011-11-26, 2012-04-27, 2012-06-08, 2013-08-26, 2014-04-13, 2014-07-17, 2.0.2, 2.0.6, 2.1.0, 2.3.2, 2.4.0 Other
Velvet velvet Milou, Rackham, Irma, Bianca 1.0.03, 1.1.04, 1.1.04_K101, 1.1.07, 1.2.10, 1.2.10_K128 GPL
wtdbg2 wtdbg2 Rackham, Irma, Bianca, Snowy 2.4 GPL v3
Bioinformatics Misc Module Cluster Version License
AdapterRemoval AdapterRemoval Milou, Rackham, Irma, Bianca 2.1.7, 2.2.2 GPL v3
AdmixTools AdmixTools Milou, Rackham, Irma, Bianca 20160803, 5.0-20170312, 5.0-20171024 Custom "as-is" open source
ADMIXTURE ADMIXTURE Milou, Rackham, Irma, Bianca 1.3.0 Not open source
ALDER alder Milou, Rackham, Irma, Bianca 1.03 Other
AlienTrimmer AlienTrimmer Milou, Rackham, Irma, Bianca 0.4.0 GPL
alleleCount alleleCount Milou, Rackham, Irma, Bianca 2.2.0, 3.2.2 GPL
ANGSD ANGSD Milou, Rackham, Irma, Bianca 0.700, 0.902, 0.917, 0.917-g6522d3e, 0.921 Open source
ANTs ANTs Rackham, Irma, Bianca, Snowy 2.3.1 Custom open-source "as is"
Artemis artemis Milou, Rackham, Irma, Bianca 15.0.0, 16.0.0 GPL
Athlates Athlates Milou, Rackham, Irma, Bianca 20140426 Custom
ATLAS ATLAS_aDNA Milou, Rackham, Irma, Bianca 20170510
ATSAS ATSAS Milou, Rackham, Irma, Bianca 2.8.3-1 Academic use only
Bamtools bamtools Milou, Rackham, Irma, Bianca 2.3.0, 2.5.1 MIT
BCFtools bcftools Milou, Rackham, Irma, Bianca 1.1, 1.2, 1.3, 1.3.1, 1.5 MIT
BclConverter Bclconverter Milou, Rackham, Irma, Bianca 1.7.1
bgc bgc Milou, Rackham, Irma, Bianca 1.03 GPL 3
bgen bgen Rackham, Irma, Bianca, Snowy 1.1.4 Boost Software License v1.0
Beagle beagle-app Milou, Rackham, Irma, Bianca 3, 4
BEETL BEETL Milou, Rackham, Irma, Bianca 1.0.2, 1.1.0 BSD 2-Clause
BioPerl BioPerl Rackham, Irma, Bianca, Snowy 1.6.924_Perl5.18.4, 1.7.1_Perl5.24.1, 1.7.2_Perl5.24.1, 1.7.2_Perl5.26.2 Perl
BioPython biopython Rackham, Irma, Bianca, Snowy 1.64 (loads python 2.7.6), 1.64-py3 (loads python 3.3.1), 1.65 (loads python 2.7.9), 1.65-py3 (loads python/3.4.3); 1.68 (loads python 2.7.6), 1.68-py3 (loads python/3.4.3); 1.73 (python/2.7.15), 1.73-py3 (python/3.6.0) Biopython
Bismark bismark Rackham, Irma, Bianca, Snowy 0.14.5, 0.15.0, 0.16.1, 0.16.2, 0.16.3, 0.18.2, 0.22.1 GPL
BreakDancer breakdancer Milou, Rackham, Irma, Bianca 1.4.4-u7, 1.4.5, 1.4.5-4e44b43 GPL 3
BRAKER braker Rackham, Irma, Bianca, milou 2.1.1_Perl5.24.1 Artistic License
BUSCO (with all lineage sets) BUSCO Milou, Rackham, Irma, Bianca 1.1b1, 1.2, 1.22, 2.0.1, 3.0.2b GPL v3+
CD-Hit aka cdhit cd-hit Milou, Rackham, Irma, Bianca 4.6.1, 4.6.4, 4.6.8-2017-1208 GPL v2
Cell Profiler cellprofiler Milou 2.1.0
Centrifuge Centrifuge Rackham, Irma, Bianca 1.0.4-beta GPL v3
CGAT CGAT Milou, Rackham, Irma, Bianca 0.3.3 "As is" 
CheckM CheckM Rackham, Irma, Bianca, Snowy 1.0.11, 1.0.12 GPL v3
CIRCexplorer CIRCexplorer Rackham, Irma, Bianca 1.1.10
CleaveLand4 CleaveLand4 Milou, Rackham, Irma, Bianca 4.3 GPL v3
cnD cnD Milou 1.3 GPL 3
CNV-seq CNV-seq Milou 20140812 Misc open source
CNVnator CNVnator Milou, Rackham, Irma, Bianca 0.3, 0.3.2, 0.3.3 Creative Commons Public License
CONCOCT CONCOCT Rackham, Irma, Bianca, Snowy 0.5.0 FreeBSD
Corset Corset Milou, Rackham, Irma, Bianca 1.04, 1.07 GPL v3
CRAM Tools cramtools Milou, Rackham, Irma, Bianca 2.0, 3.0
deepTools deepTools Rackham, Irma, Bianca 1.5.11 (milou only), 2.0.1, 2.2.3, 2.3.1, 2.4.3, 2.5.1, 3.1.0 GPL v3
DosageConvertor DosageConvertor rackham, irma, bianca, snowy 1.0.4 custom
DWGSIM DWGSIM Milou, Rackham, Irma, Bianca 0.1.11-6e9a361 GPL v2
EEMS eems Milou, Rackham, Irma, Bianca 20160605 Misc open source
EIGENSOFT eigensoft Milou, Rackham, Irma, Bianca 4.2, 5.0.1, 6.0.1 (long ID support), 6.1.2 (default ID).  All following have long ID support. 6.1.4, 7.2.0, 7.2.1 Custom
EMIRGE emirge Milou, Rackham, Irma, Bianca 0.60 GPL
EMMAX emmax Milou, Rackham, Irma, Bianca Beta-07Mar2010 GPL
EnsEMBL Perl API EnsEMBL-API Milou 87 Modified Apache
EPACTS EPACTS Milou, Rackham, Irma, Bianca 3.2.6, 3.3.0-a5209db GPL v3
ExpansionHunter ExpansionHunter Milou, Rackham, Irma, Bianca 2.5.3 GPL v3
eXpress eXpress Milou, Rackham, Irma, Bianca 1.5.1 Artistic License 2.0
fastNGSadmix fastNGSadmix Milou, Rackham, Irma, Bianca 20170825-099ab7f
fastPHASE fastPHASE Milou, Rackham, Irma, Bianca 1.4.0, 1.4.8 Executable only
FastQC FastQC Rackham, Irma, Bianca, Snowy 0.11.2, 0.11.5, 0.11.8 GPL
fastq_screen fastq_screen Milou, Rackham, Irma, Bianca 0.3.1, 0.4.3. 0.5.1, 0.9.2, 0.11.1 GPL
FASTX Fastx Milou, Rackham, Irma, Bianca 0.0.13, 0.0.13.2, 0.0.14 AGPLv3
Filtlong Filtlong Rackham, Irma, Bianca, Snowy 0.2.0-20190515-13504b7 GPL v3
fineSTRUCTURE fineSTRUCTURE Rackham, Irma, Bianca, Snowy 4.0.1 Free for noncommercial use only
FLASH FLASH Milou, Rackham, Irma, Bianca 1.2.11 GPL
flashpca flashpca Milou 1.1.2.1 GPL
fqzcomp fqzcomp Milou, Rackham, Irma, Bianca 4.6
FreeBayes freebayes Milou, Rackham, Irma, Bianca 0.8.9, 0.9.4, 0.9.4_2012-04-16, 0.9.8, 0.9.21, 1.0.2, 1.1.0 Custom open-source "as-is"
FusionCatcher FusionCatcher Rackham, Irma, Bianca, Snowy 1.00, 1.10 GPL
GAM-NGS gam-ngs Milou 1.1b GPL
GCTA gcta Milou, Rackham, Irma, Bianca 0.92.0, 0.92.6, 0.93.9, 1.26.0 Public domain
GEM GEM Rackham, Irma, Bianca, Snowy 2.7, 3.4 "Research only"
GEMMA GEMMA Rackham, Irma, Bianca, Snowy 0.98.1 GPL3
GeneMark GeneMark Milou, Rackham, Irma, Bianca 2.3-es (Milou), 4.32-es, 4.33-es Other
GenomeTools GenomeTools Milou 1.3.5 (Milou), 1.5.8 BSD style
GERP++ GERP++ Milou 20110522 GPL v3+
GTOOL GTOOL Milou 0.7.5 "As is" open source
gvcftools gvcftools Milou, Rackham, Irma, Bianca 0.16.2, 0.17.0 Various "As Is" open source
HiCExplorer HiCExplorer Milou, Rackham, Irma, Bianca 2.2-beta GPL v3
HiCUP HiCUP Rackham, Irma, Bianca, Snowy 0.7.2 GPL v3 or later
HTSlib htslib Milou, Rackham, Irma, Bianca

1.2.1, 1.3, 1.3.2, 1.4, 1.5, 1.6,
1.8 (Bianca, Irma, Rackham)

MIT
HTSeq htseq Milou, Rackham, Irma, Bianca 0.4.6, 0.5.1. 0.6.1, 0.9.1 GPL
Integrative Genomics Viewer IGV Milou, Rackham, Irma, Bianca 1.5.51, 2.3.17, 2.3.40, 2.3.92, 2.4.2 LGPL
Integrative Genomics Viewer Tools IGVtools Milou, Rackham, Irma, Bianca 2.2.1, 2.3.17, 2.3.40, 2.3.91, 2.3.98 LGPL
IM IM Milou 20091217
IMa2p IMa2p Milou 2015-08-09 GPL v3
IMPUTE2 IMPUTE2 Milou, Rackham, Irma, Bianca 2.3.2 "As is" open source
ITSx ITSx Milou, Rackham, Irma, Bianca 1.0.9, 1.0.11, 1.1-beta GPL
Jellyfish jellyfish Milou, Rackham, Irma, Bianca 1.1.11, 2.0.0, 2.1.4, 2.2.3-dev, 2.2.4, 2.2.6 GPL
kallisto kallisto Rackham, Irma, Bianca, Snowy 0.42.4, 0.43.0, 0.43.1, 0.45.1 Custom "as is" open source
KAT KAT Rackham, Irma, Bianca, Snowy 2.0.4, 2.0.6, 2.0.8, 2.1.1, 2.3.4, 2.4.2, 2.4.2_py3.7.2 GPL v3
Khmer khmer Milou, Rackham, Irma, Bianca 1.4, 2.0, 2.1.1
KmerGenie KmerGenie Milou, Rackham, Irma, Bianca 1.6741, 1.7039 Other
Kraken Kraken Milou, Rackham, Irma, Bianca 0.10.5-beta, 1.0, 1.1-352e780 GPL v3
Kraken2 Kraken2 Rackham, Irma, Bianca, Snowy 2.0.7-beta-bc14b13, 2.0.8-beta MIT
KrakenHLL KrakenHLL Rackham, Irma, Bianca 0.4.9
Krona Krona Milou, Rackham, Irma, Bianca 2.7 Custom open source
LASER LASER Rackham, Irma, Bianca, Snowy 2.01, 2.02, 2.04 GPL v3
Latent Strain Analysis LatentStrainAnalysis Milou 20160322 (fork of a fork) MIT
LDhelmet LDhelmet Rackham, Irma, Bianca, Snowy 1.7, 1.9, 1.10 GPL v3
liftOver liftOver Rackham, Irma, Bianca, Snowy 2017-03-14
LTR_Finder LTR_Finder Rackham, Irma, Bianca, Snowy 1.0.5, 1.0.7 Free for non-commercial use
LUMPY LUMPY Milou, Rackham, Irma, Bianca 0.2.12, 0.2.13-213a417 MIT
MACS MACS

Milou; Rackham, Irma, Bianca

1.4.1, 1.4.2, 2.1.0; 2.1.2

Other
MACE MACE Milou 1.2
MAGeCK MAGeCK Milou, Rackham, Irma, Bianca 0.5.6 BSD 3-clause
MALDER malder Rackham, Irma, Bianca 1.0
manta manta Milou 0.27.1, 1.0.0, 1.0.3 GPL v3
mapDamage mapDamage Milou, Rackham, Irma, Bianca 2015-04-10 Public Domain
matrix2png matrix2png Milou 1.2.1 Apache
MaxBin MaxBin Rackham, Bianca, Irma, Snowy 2.2.5 BSD
medaka medaka Rackham, Bianca, Irma, Snowy 0.7.1 MPL 2.0
Meerkat Meerkat Milou 0.189 Misc non-commercial open source
MELT MELT Milou, Rackham, Irma, Bianca 2.0.2 Misc non-commercial
mergeSVcallers mergeSVcallers Milou, Rackham, Irma, Bianca 161006-23533ef
MetaBAT MetaBat Milou, Rackham, Irma, Bianca 0.26.3, 2.12.1 BSD-like
MetaSV MetaSV Milou, Rackham, Irma, Bianca 0.5.4 BSD 2-clause
Metaxa2 Metaxa2 Milou 2.1.3 GPL v3
MethPipe MethPipe Milou, Rackham, Irma, Bianca 3.4.3 GPL v3+
MethylDackel MethylDackel Milou, Rackham, Irma, Bianca 0.2.1
MHC-PRG MHC-PRG Rackham, Irma, Bianca, Snowy 1.00 GPL v3
micca micca Milou 1.4.0 GPL v3
Mimar mimar Milou 20101217
Minimac4 Minimac4 Rackham, Irma, Bianca, Snowy 1.0.0 GPL v3
miRDeep2 mirdeep2 Milou, Rackham, Irma, Bianca 2.0.0.5, 2.0.0.8
MMSEQ mmseq Milou 1.0.8a GPL
Mothur Mothur Rackham, Irma, Bianca, Snowy 1.40.5, 1.41.0 GPL v3
MSMC msmc Milou, Rackham, Irma, Bianca 2014-09-29, 0.1.0 GPL
MultiQC MultiQC Rackham, Irma, Bianca, Snowy 0.3.1, 0.3.1-py3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.2, 1.3, 1.5, 1.6, 1.7 MIT
MuSIC2 music2 Rackham,Irma,Bianca, Snowy 0.2 MIT
MuTect mutect Milou, Rackham, Irma, Bianca 1.1.5 Other
NGSadmix NGSadmix Milou, Rackham, Irma, Bianca 32
ngsplot ngsplot Milou, Rackham, Irma, Bianca 2.61 GPL v2
NGSrich ngsrich Milou, Rackham, Irma, Bianca 0.7.8
NGSUtils NGSUtils Milou, Rackham, irma, Bianca 0.5.9 Custom open source "as is"
nibabel nibabel Rackham, Irma, Bianca, Snowy 2.3.3 MIT + BSD
OpenMS OpenMS Milou 2.0.0 BSD + other
OptiType OptiType Milou, Rackham, Irma, Bianca 1.3.1 BSD 3-Clause
OrthoMCL OrthoMCL Milou, Rackham, Irma, Bianca 2.0.9
PEAR pear Milou, Rackham, Irma, Bianca 0.9.5, 0.9.10 CC
PennCNV PennCNV Milou 20151014 Public domain
Pftools pftools Milou 2.3
phantompeakqualtools phantompeakqualtools Milou, Rackham, Irma, Bianca 1.1 MIT
PhyloPhlAn phylophlan Milou, Rackham, Irma, Bianca 0.99 Custom "as is" open source
Picard picard Rackham, Irma, Bianca, Snowy 1.92, 1.118, 1.141, 2.0.1, 2.10.3, 2.19.2, 2.20.4 MIT
PileOMeth (continued by MethylDackel) PileOMeth Milou 0.1.13
Pindel pindel Milou 0.2.4w GPL 3
PLINK plink Milou, Rackham, Irma, Bianca 1.07, 1.90b3n (formerly version 1.90), 1.90b4.9, 2.00-c1defe4 GPL v3
PLINK/SEQ plinkseq Milou, Rackham, Irma, Bianca 0.08 (formerly mislabelled as 0.8), 0.10 Other
Porechop Porechop Rackham, Irma, Bianca, Snowy 0.2.4 GPL v3
Poretools poretools Milou 0.5.1-devel Open source
Preseq preseq Milou, Rackham, Irma, Bianca 0.1.0, 2.0 GPL
Primer3 Primer3 Milou, Rackham, Irma, Bianca 2.3.7 GPL v2
PRINSEQ prinseq Rackham, Irma, Bianca, Snowy 0.20.4
Prodigal prodigal Milou, Rackham, Irma, Bianca 2.60, 2.6.3 GPL v3
ProtExcluder ProtExcluder Milou, Rackham, Irma, Bianca 1.1
PSMC psmc Rackham, Irma, Bianca, Snowy 0.6.5-r67-e5f7df5 MIT
PSORTb psortb Milou 3.0 GPL
pyGenomeTracks pyGenomeTracks Rackham, Irma, Bianca, Snowy 2.1 GPL v3
PySam pysam Milou, Rackham, Irma, Bianca 0.6, 0.7.7 (Python2 & 3), 0.8.3 (python 2.7.6), 0.8.3-py27 (python 2.7), 0.8.3-py3 (python 3.4.3), 0.9.1.4, 0.10.0, 0.13-python2.7.11, 0.13-python3.6.0 MIT
qctool qctool Rackham, Irma, Bianca, Snowy 1.4, 2.0.1 "As is" open source
QuantiSNP QuantiSNP Milou 2.2
QUAST quast Milou, Rackham, Irma, Bianca 2.2, 2.3, 3.2, 4.5.4
QuorUM QuorUM Rackham, Irma, Bianca, Snowy 1.0.0 GPL v3
RDP Classifier rdp-classifier Rackham, Irma, Bianca, Snowy 2.2, 2.4
RDXplorer RDXplorer Rackham, Irma, Bianca, Snowy 3.2 open source
RegScan RegScan Rackham, Irma, Bianca, Snowy 0.5 open source
RepeatMasker RepeatMasker Rackham, Irma, Bianca, Snowy 4.0.7, 4.0.7_Perl5.24.1, 4.0.8 open source
RepeatModeler RepeatModeler Rackham, Irma, Bianca, Snowy 1.0.8_RM4.0.7, 1.0.11 open source
RGT RGT Rackham, Irma, Bianca, Snowy 0.11.6 GPL v3+
Roary Roary Rackham, Irma, Bianca, Snowy 3.6.2, 3.12.0 GPL v3
RSEM rsem Milou 1.2.12, 1.2.29 GPL
RSeqC rseqc Milou, Rackham, Irma, Bianca 2.3, 2.3.6, 2.3.9, 2.4, 2.6.1, 2.6.4
RTG Core non-commercial (aka rtg-core) rtgcore Milou, Rackham, Irma, Bianca 3.8.3 Custom non-commercial use only
RTG Tools (aka rtg-tools) rtgtools Milou, Rackham, Irma, Bianca (3.10.1 Sowy, Rackham, Irma, Bianca) 3.7.1, 3.8.1, 3.8.3, 3.10.1 BSD
Sailfish Sailfish Milou 0.8.0 GPL v3+
Salmon Salmon Milou, Rackham, Irma, Bianca 0.6.0, 0.8.2, 0.9.1 GPL v3+
sambamba sambamba Milou, Rackham, Irma, Bianca 0.5.9, 0.6.6 GPL v2+
samblaster samblaster Milou, Rackham, Irma, Bianca 0.1.22, 0.1.24 MIT
samplefq samplefq Milou, Rackham, Irma, Bianca 0.2 GPL v3
samstat samstat Rackham, Irma, Bianca 1.5.1 GPL v3
SAMtools samtools Milou, Rackham, Irma, Bianca 0.1.7a, 0.1.8, 0.1.9, 0.1.12, 0.1.16, 0.1.18, 0.1.19, 1.1, 1.2, 1.3, 1.4, 1.5 MIT
SBT (bloomtree) SBT Milou, Rackham, Irma, Bianca 0.1, 0.3
Scalpel scalpel Milou, Rackham, Irma, Bianca 0.5.2, 0.5.3 MIT
Schmutzi schmutzi Milou 20160424
SCORE-Seq SCORE-Seq Milou 5.3
Selscan selscan Milou, Rackham, Irma, Bianca 1.1.0 GPL v3
SeqAn SeqAn Milou, Rackham, Irma, Bianca 1.4.2 Other open-source
seqMINER seqMINER Milou 1.3.3e
seqtk seqtk Milou, Rackham, Irma, Bianca 1.0-r31, 1.0-r57, 1.0-r68e, 1.2-r101 MIT
SeqMonk seqmonk Milou, Rackham, Irma, Bianca 0.21.0, 0.27.0, 0.32.1, 0.34.1, 1.36.0, 1.37.1 GPL
SeqPrep SeqPrep Milou, Rackham, Irma, Bianca 1.1 (formerly 2013-11-14), 1.2 MIT
SeqTools SeqTools Milou, Rackham, Irma, Bianca 4.20, 4.44.1 Apache 2.0
SHAPEIT SHAPEIT Milou, Rackham, Irma, Bianca v2.r837 Custom non-commercial
ShoRAH ShoRAH Milou, Rackham, Irma, Bianca 1.1.0 GPL v3
SHORE SHORE Milou, Rackham, Irma, Bianca 0.9.3 GPL v3
sickle sickle Milou, Rackham, Irma, Bianca 1.210, 1.33-20-g4b0dc85-mullins Other
SLiM SLiM Rackham, Irma, Bianca, Snowy 3.2.1 GPL v3
snap snap Milou, Rackham, Irma, Bianca 2013-02-16, 2013-11-29 GPL
snippy snippy Milou, Rackham, Irma, Bianca 4.0, 4.0.5 GPL 2.0
SNPTEST SNPTEST Rackham, Irma, Bianca, Snowy 2.5.2, 2.5.5 "As is" open source
SomaticSeq SomaticSeq Milou 1.2.1 Other
SPP SPP Rackham, Irma, Bianca, Snowy 1.11 GPL v2
SRA Toolkit sratools Rackham, Irma, Bianca, Snowy 2.5.7, 2.8.0, 2.8.2-1, 2.9.1-1, 2.9.6-1 Public domain
Stacks Stacks Rackham, Irma, Bianca, Snowy 1.12, 1.19, 1.21, 1.22, 1.24, 1.29, 1.34, 1.35, 1.40, 1.48, 2.0Beta9, 2.0b, 2.2 GPL v3
Stargazer Stargazer Rackham, Irma, Bianca, Snowy 1.0.4 GPL v3
strelka strelka Milou, Rackham, Irma, Bianca 1.0.15 GPL v3
Strelka2 Strelka2 Milou, Rackham, Irma, Bianca 2.8.4 GPL v3
Subread subread Milou, Rackham, Irma, Bianca 1.4.5, 1.4.5-p, 1.5.0, 1.5.1, 1.5.2 GPL
SVDetect SVDetect Milou 0.8b
SVMerge SVMerge Milou 1.2r37 Open source "as is"
svprops svprops Milou, Rackham, Irma, Bianca 20171020-ebf6762 GPL v3+
tabix (includes bgzip) tabix (Note: more recent versions in htslib module) Milou, Rackham, Irma, Bianca 0.2.6 MIT/Expat
Tablet Tablet Milou, Rackham, Irma, Bianca 1.15.09.01 Custom "as is" redistributable
Tassel Tassel Milou 3.0, 5.0
tbl2asn tbl2asn Milou, Rackham, Irma, Bianca 25.3
TE-Tracker TE-Tracker Milou 20141124
TEtools TEtools Milou, Rackham, Irma, Bianca 1.0.0-283c1ca GPL v3
TIDDIT TIDDIT Milou, Rackham, Irma, Bianca 2.3.0 GPL v3
transfuse tranfuse Milou, Rackham, Irma, Bianca 0.5.0 MIT
Transrate transrate Rackham, Irma, Bianca, Snowy 1.0.1, 1.0.2, 1.0.3 MIT
TreeMix TreeMix Milou, Rackham, Irma, Bianca 1.12 GPL v3
Trim Galore! TrimGalore Rackham, Irma, Bianca, Snowy 0.4.0, 0.4.1. 0.4.4, 0.6.1 GPL v3
Trimmomatic trimmomatic Milou, Rackham, Irma, Bianca 0.32, 0.36 GPL
TSC TSC Milou, Rackham, Irma, Bianca 1.2
UCSC Bioinformatics Utilities ucsc-utilities Milou, Rackham, Irma, Bianca v287, v334, v345 Other
UMI-tools umi_tools Rackham, Irma, Bianca, Snowy 0.5.3, 0.5.4, 1.0.0 MIT
usearch (32-bit version) usearch Milou, Rackham, Irma, Bianca 5.2.236, 5.2.32, 6.1.544, 7.0.1090, 8.1.1861, 9.2.64 Other
VarDictJava VarDictJava Milou, Rackham, Irma, Bianca 1.4.5 MIT
VarScan VarScan Milou, Rackham, Irma, Bianca 2.3.6, 2.3.7, 2.4.2 NPOSL
VAT VAT Milou, Rackham, Irma, Bianca 2.0.1 Other open-source
VCFaid VCFaid Milou, Rackham, Irma, Bianca 20170616-f0732ae GPL v3
vcflib vcflib Milou, Rackham, Irma, Bianca 2014-07-22 (milou only), 2016-08-29, 2017-04-04 MIT
Variant Effect Predictor from Ensembl Tools vep Milou, Rackham, Irma, Bianca 82, 84, 86, 87, 89, 91, 92 Modified Apache
verifyBamID verifyBamID Rackham, Irma, Bianca, Snowy 1.1.2, 1.1.3 GPL v3, and others
VerifyBamID2 VerifyBamID2 Rackham, Irma, Bianca, Snowy 1.0.6
ViennaRNA RNAfold (ViennaRNA is an alias) Milou, Rackham, Irma, Bianca 1.8.4, 2.1.8, 2.2.5, 2.3.1 Custom "as is" open source
vt vt Milou, Rackham, Irma, Bianca 0.5772 MIT
Bioinformatics Phylogeny Module Cluster Version License
beagle-lib beagle Milou, Rackham, Irma, Bianca 1.0.0, 2.1.2 GPL
BEAST beast Milou, Rackham, Irma, Bianca 1.7.5, 1.8.1, 1.8.4 GPL
BEAST2 beast2 Milou, Rackham, Irma, Bianca 2.1.2, 2.3.1, 2.4.0, 2.4.8 LGPL v2.1
Concaterpillar concaterpillar Milou 1.4, 1.8a
CONSEL CONSEL Milou, Rackham, Irma, Bianca 0.20
ExaBayes ExaBayes Rackham, Irma, Bianca, Snowy 1.5, 1.5-mpi GPL v3
FastML FastML Milou, Rackham, Irma, Bianca 3.1
FastTree FastTree Milou, Rackham, Irma, Bianca 2.1.8, 2.1.10 Open source "as is"
GARLI garli Milou, Rackham, Irma, Bianca 2.1 GPL v3
Gubbins gubbins Milou, Rackham, Irma, Bianca 1.4.2, 2.3.1 GPL v2
HyPhy HyPhy Rackham, Irma, Bianca, Snowy 2.5.0, 2.5.0-mpi Custum open-source "as is"
IQ-TREE iqtree Rackham, Irma, Bianca, Snowy 1.4.3-pomp, 1.5.3-omp, 1.5.4-omp-mpi, 1.6.5-omp-mpi, 1.6.10-omp-mpi, 1.6.12-omp-mpi GPL v2
MEGAN MEGAN Milou, Rackham, Irma, Bianca 4.70.4, 5.1.5, 5.11.3, 6.3.5, 6.10.5 Personal academic
MetaPhlAn2 metaphlan2 Rackham, Irma, Bianca, Snowy 2.0
MrBayes mrbayes Milou, Rackham, Irma, Bianca 3.1.2-mpi, 3.2.20 (mpi), 3.2.1 (mpi), 3.2.3a (mpi), 3.2.4 (mpi), 3.2.6 (mpi), 3.2.6 with gcc 7.1.0 (mpi) Public domain
NEXUS Class Library ncl Milou, Rackham, Irma, Bianca 2.1.21-dev Simplified BSD
PAML paml Milou, Rackham, Irma, Bianca 4.6, 4.9e Other
Phast phast Rackham, Irma, Bianca, Snowy 1.4, 1.5 BSD
PhyloBayes phylobayes Milou, Rackham, Irma, Bianca 4.1c
PhyloBayes MPI phylobayesmpi Milou, Rackham, Irma, Bianca 1.3b, 1.4f, 1.5a, 1.7a, 1.8 GPL v2
PhyML PhyML Rackham, Irma, Bianca, Snowy 3.1, 3.3.20190321 GPL v3
Phyutility phyutility Rackham, Irma, Bianca, Snowy 2.7.3
RAxML raxml Rackham, Irma, Bianca, Snowy 7.0.4, 7.2.7, 7.2.8, 7.4.7, 8.0.20, 8.0.20-mpi, 8.2.0-gcc, 8.2.0-icc, 8.2.0-gcc-mpi, 8.2.0-icc-mpi, 8.2.4-gcc, 8.2.4-gcc-mpi, 8.2.10-gcc, 8.2.10-gcc-mpi GPL
RAxML-NG RAxML-NG Rackham, Irma, Bianca, Snowy 0.2.0b, 0.2.0b-mpi, 0.7.0b, 0.7.0b-mpi, 0.9.0, 0.9.0-mpi GNU Affero GPL v3.0
Yleaf Yleaf Rackham, Irma, Bianca, Snowy 20180326, 2.0
Bioinformatics Pipelines Module Cluster Version License
ab_wtp ab_wtp Milou 1.1 (modified for SLURM) GPL
bpipe bpipe Rackham, Irma, Bianca, Snowy 0.9.8.6, 0.9.8.7 BSD
Bowtie bowtie Rackham, Irma, Bianca, Snowy 0.12.9, 1.1.2, 1.2.0, 1.2.2, 1.2.3 Artistic
Bowtie2 bowtie2 Rackham, Irma, Bianca, Snowy 2.1.0, 2.2.9, 2.3.2, 2.3.3.1, 2.3.4.1, 2.3.4.3, 2.3.5.1 GPL v3
Cluster Flow clusterflow Rackham, Irma, Bianca, Snowy 0.3, 0.4devel, 0.4 GPL v3
Cufflinks cufflinks Rackham, Irma, Bianca, Snowy 2.1.1, 2.2.1, 2.2.1-b55bb21 Boost License v1.0
cutadapt cutadapt Rackham, Irma, Bianca, Snowy 1.9.1, 1.13, 1.16, 2.0, 2.3 MIT
DeepVariant DeepVariant Rackham, Irma, Bianca, Snowy 0.8.0 BSD-3
fermikit fermikit Rackham, Irma, Bianca, Snowy r178, 0.14-prerelease-96f7820
HiC-Pro HiC-Pro Rackham, Irma, Bianca, Snowy 2.11.1 BSD-3
hichipper hichipper Rackham, Irma, Bianca, Snowy 0.7.3 MIT
MIP mip Rackham, Irma, Bianca, Snowy 6.0.0 MIT
Nextflow Nextflow Rackham, Irma, Bianca, Snowy 18.10.1
Qiime Qiime Milou, Rackham 1.4.0, 1.5.0, 1.6.0, 1.8.0, 1.9.1
qiime2 qiime2 Rackham, Irma, Bianca, Snowy 2018.11.0 BSD 3
SMRT Link, SMRT Analysis SMRT Rackham, Irma, Bianca, Snowy 2.2.0, 2.3.0, 5.0.1, 7.0.1
snakemake snakemake Milou, Rackham, Irma, Bianca 3.10.1, 4.5.0, 5.2.3, 5.4.5
Tophat tophat Milou, Rackham, Irma, Bianca 1.0.14, 1.1.0, 1.1.3, 1.2.0, 1.3.3, 1.4.0, 2.0.0, 2.0.3, 2.0.4, 2.0.8b, 2.0.10, 2.0.11, 2.0.12, 2.1.1
Bioinformatics SW Collections Module Cluster Version License
454-dataanalysis (Roche Newbler assembler) 454-dataanalysis Rackham, Irma, Bianca, Snowy 2.3, 2.53, 2.6, 2.9
454-dataprocessing 454-dataprocessing Rackham, Irma, Bianca, Snowy 2.3
ANNOVAR annovar Rackham, Irma, Bianca, Snowy

2014.11.12, 2015.06.17, 2016.05.11, 2017.07.16, 2018.04.16

Strictly non-commercial usage
ART ART rackham, irma, bianca, snowy 2016-06-05
BBMap bbmap Rackham, Irma, Bianca, Snowy 33.41, 35.14, 35.40, 37.53, 38.08, 38.61b Other
bcl2fastq bcl2fastq Milou, Rackham, Irma, Bianca 1.8.3 (milou), 1.8.4, 2.15.0, 2.16.0, 2.17.1, 2.20.0
BEDOPS BEDOPS Milou, Rackham, Irma, Bianca 2.4.3, 2.4.28 GPL v2
BEDTools BEDTools Milou, Rackham, Irma, Bianca 2.10.0, 2.11.2, 2.16.2, 2.20.1, 2.21.0, 2.23.0, 2.25.0, 2.26.0, 2.27.1 GPL
bioscope bioscope Milou 1.2.1, 1.3.1 Commercial
CASAVA CASAVA Milou, Rackham, Irma, Bianca 1.7.0, 1.8.2
Chipster chipster Rackham, Irma, Bianca, Snowy webstart
Cell Ranger (Chromium 10X) cellranger Rackham, Irma, Bianca, Snowy 1.1.0, 1.3.0, 2.0.2, 3.0.1 other
EMBOSS emboss Milou 6.3.1, 6.4.0, 6.5.7 GPL
GATK GATK Rackham, Irma, Bianca, Snowy 3.5.0, 3.6, build-20160727, 3.7, 3.8-0, 4.beta.5,

4.1.0.0, 4.1.1.0

BSD Style
GATK-Queue GATK-Queue Milou, Rackham, Irma, Bianca 3.2.2, 3.6, 3.7, 3.8-0 MIT + academic non-commercial
GenomeSTRiP GenomeSTRiP Milou, Rackham, Irma, Bianca 2.00.1650, 2.00.1685, 2.00.1710 Custom 'as is' redistributable
HiSeq HiSeq Milou 0.9
Long Ranger (Chromium 10X) longranger Rackham, Irma, Bianca, Snowy 2.0.1, 2.1.1, 2.1.2, 2.1.4, 2.2.2 other
MEME Suite MEMEsuite Milou 4.11.1, 4.11.2_1 BSD Style
SpeedSeq SpeedSeq Milou, Rackham, Irma, Bianca 0.1.0-20151121, 0.1.2-20170504-30f8dc6 MIT
Staden staden Milou 2.0.0b6 BSD
Supernova (Chromium 10X) supernova Milou, Rackham, Irma, Bianca 1.0.0, 1.1.1, 1.1.4, 2.0.0 other
VCFtools vcftools Milou, Rackham, Irma, Bianca 0.1.8a, 0.1.11, 0.1.12, 0.1.13, 0.1.14, 0.1.15 GPL