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".

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 UPPMAX clusters, 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
bison bison Rackham, Irma, Bianca, Snowy 3.7.6 GPL v3+
bubblewrap bubblewrap Rackham, Irma, Bianca, Snowy, Miarka 0.6.2 LGPL v2+
flex flex Rackham, Irma, Bianca, Snowy 2.6.4 modified BSD
Free Pascal Compiler fpc Rackham, Irma, Bianca, Snowy 3.0.4 GPL and LGPL
Gnu binutils binutils Rackham, Irma, Bianca, Snowy 2.28, 2.38 GPL v2, v3; LGPL v2, v3
gcc gcc Rackham, Irma, Bianca, Snowy 4.x, 5.x, 6.x, 7.x, 8.x, 9.x, 10.x, 11.x GPL
Git git Rackham, Irma, Bianca, Snowy 2.5.0, 2.10.2, 2.16.1, 2.21.0, 2.24.0, 2.28.0, 2.34.1 LGPL 2.1
Git Large File Support git-lfs Rackham, Irma, Bianca, Snowy 2.9.1 MIT
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, Miarka, Bianca, Snowy 1.0.4_LTS, 1.1.1, 1.4.2, 1.6.1, 1.6.3, 1.6.7_LTS, 1.7.2, 1.8.5 MIT
k8 k8 Rackham, Irma, Bianca, Snowy 0.2.5
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, 0.57.2 Apache 2.0
Mono mono Rackham, Irma, Bianca, Snowy 3.12.0, 5.8.1.0, 5.10.1.27 Custom open source
NASM nasm Rackham, Irma, Bianca, Snowy 2.15.05 BSD 2-clause
Ninja ninja Rackham, Irma, Bianca, Snowy 1.9.0, 1.10.0 Apache 2.0
patchelf patchelf Rackham, Irma, Bianca, Snowy 0.8, 0.10 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, 3.8.7, 3.9.5, 3.10.8 PSF License Agreement
Python 3 (does not conflict with python module) python3 Rackham, Irma, Bianca, Snowy 3.6.0, 3.6.8, 3.7.2, 3.8.7, 3.9.5, 3.10.8 PSF License Agreement
Ruby ruby Rackham, Irma, Bianca, Snowy 2.4.1, 2.5.0, 2.6.2 Ruby license
Rust rust Rackham, Irma, Bianca, Snowy 1.43.1 Apache 2.0, MIT
Subversion subversion Rackham, Irma, Bianca, Snowy 1.9.3 Apache 2.0
Yasm yasm Rackham, Irma, Bianca, Snowy 1.3.0 'new' BSD
Chemistry/Physics
ABINIT ABINIT Rackham, Irma, Bianca, Snowy 8.10.3 GPL v3
ALPS including Boost ALPS Rackham, Irma, Bianca, Snowy 2.3.0 ALPS Library licence 1.0, Application licence 1.0: acad/non-comm only
DOCK DOCK Rackham, Irma, Bianca, Snowy 3.7 Free Academic License
Gaussian
 
g03
g09
Milou, Tintin
Rackham, Snowy
g03.d02, g03.e01,
09.a02, g09.c01, g09.d01
UU site license
ORCA ORCA Rackham, Snowy, (Bianca) 5.0.2, 4.2.1, 4.0.1.2 Free Academic License
turbomole turbomole Rackham, Irma, Bianca, Snowy 7.3 proprietary group license
TmoleX TmoleX Rackham, Irma, Bianca, Snowy 18 proprietary group license
gamess gamess Milou,
Rackham
20110811R1 20101001R1 20070324R1, 20170930 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
MOLDEN molden Rackham 5.1
PRISMS-PS PRISMS-PF Rackham, Snowy 2.1.1 Lesser GPL
VMD VMD Rackham, Snowy, Bianca, Miarka 1.9.3, 1.9.4-alpha-57 University of Illinois Open Source License
Engineering
Matlab matlab Milou, Rackham, Snowy, Bianca, Irma 7.4, 7.8, 7.10, 7.13, 8.0, 8.1, R2014a, R2015a, R2015b, R2016a, R2017a, R2018a, R2018b, R2019a, R2020b site license
envi envi Milou 4.8
openfoam OpenFOAM Rackham, Snowy 2.4.0, v1612+, v1912, 4.1, 4.1-waves2Foam, 6, 7
Comsol comsol Rackham, Snowy, Bianca 4.4, 5.2a, 5.3, 5.4, 5.5, 5.6, 6.0 UU site license
Geospatial
CDO CDO Rackham, Irma, Bianca, Snowy 1.9.5, 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, 3.1.0 X/MIT style Open Source
GEOS GEOS Rackham,Bianca, Snowy, Miarka 3.5.0, 3.9.1-gcc9.3.0, 3.11.0-gcc10.3.0 LGPL v2.1
GOTM GOTM Rackham, Irma, Bianca, Snowy 5.3-221-gac7ec88d GPL v2
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
NCL NCL-graphics Rackham 6.6.2 Apache 2.0
NCO NCO Rackham, Irma, Bianca, Snowy 4.8.1, 4.9.2, 4.9.3 BSD
ncview ncview Rackham, Irma, Bianca, Snowy 2.1.7 GPL v3
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
PROJ PROJ Rackham, Irma, Bianca, Snowy 6.3.2, 8.1.0, 9.1.1 MIT
GIS_packages for python python_GIS_packages Rackham, Miarka, Bianca, Snowy 3.10.8 ----
QGIS QGIS Rackham, Irma, Bianca, Snowy 3.4.12 GPL
SHAPELIB SHAPELIB Rackham, Irma, Bianca, Snowy 1.5.0 LGPL v2
Vapor Vapor Rackham, Snowy 3.2.0, 3.3.0 Apache v2.0 license
WRF/WPS WRF & WPS Rackham, Snowy 4.1.3, 4.3.1 Custom open-source AS IS
wrf-python wrf-python Rackham, Snowy 1.3.1 GPL v2
Statistics
JAGS JAGS Rackham, Irma, Bianca, Snowy 4.2.0, 4.3.0 GPL v2
MultiBUGS MultiBUGS Rackham, Irma, Bianca, Snowy 2.0 LGPL v3.0
NONMEM nonmem Rackham, Irma, Bianca, Snowy 7.4.3, 7.4.3-intel, 7.4.4, 7.5.0 commercial
Perl-speaks-NONMEM PsN Rackham, Irma, Bianca, Snowy 5.0.0, 5.2.6, 5.3.0 GPL v2+
R R Rackham, Irma, Bianca, Snowy 3.0.2, 3.2.3, 3.3.2, 3.4.0, 3.4.3, 3.5.0, 3.5.2, 3.6.0, 3.6.1, 4.0.0, 4.0.4, 4.1.1 GPL
R packages, includes nearly all packages in 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, 4.0.0, 4.0.4, 4.1.1 GPL, LGPL. and others
RStudio RStudio Rackham, Irma, Bianca, Snowy, Miarka 1.0.136, 1.0.143, 1.0.153, 1.1.423, 1.1.463, 1.4.1106, 2022.02.0-443, 2022.02.3-492, 2022.07.1-554 Custom
stata stata Milou 12, 14
Misc Applications
agrep agrep Rackham, Irma, Bianca, Snowy 3.41.5 ISC Open Source
albacore albacore Rackham, Irma, Bianca, Snowy build-4aee41d GPL3
Alphafold alphafold Rackham, Irma, Bianca, Snowy 2.0.0 Apache License
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, Miarka 3.5.1, 3.7.2, 3.13.2, 3.17.3, 3.22.2 BSD 3-Clause
COIN-OR Optimization Suite COIN-OR-OptimizationSuite Rackham, Irma, Bianca, Snowy 1.8.0
Cowsay cowsay Rackham, Irma, Bianca, Snowy 3.03 Artistic License
CPLEX Optimization Studio CPLEXOptimizationStudio Rackham, Irma, Bianca, Snowy, Miarka 12.9.0, 20.10 IBM Academic
Cromwell Cromwell Rackham, Irma, Bianca, Snowy 71 BSD 3-Clause
Doxygen doxygen Rackham, Irma, Bianca, Snowy 1.8.11 Gnu GPL 2
eLSA eLSA Rackham, Irma, Bianca, Snowy eLSA/20160907-febe2d7a57c8
FFmpeg FFmpeg Rackham, Irma, Bianca, Snowy 4.4 LGPL v2.1+ with non-free features
Ghostscript, GhostPCL, GhostXPS, GhostPDL GhostPDL Rackham, Irma, Bianca, Snowy 9.53.3 Gnu GPL Affero v3
Gnu Data Language gdl Rackham, Irma, Bianca, Snowy 1.0.0-rc.1 GPL v2
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"
Graphviz Graphviz Rackham, Irma, Bianca, Snowy 2.40.1
groff groff Rackham, Irma, Bianca, Snowy 1.22.3 GPL
h5utils h5utils Rackham, Irma, Bianca, Snowy 1.12.1 GPL v2+
Haskell Tool Stack haskell-stack Rackham, Irma, Bianca, Snowy 1.0.4.3, 1.4.0 Custom "as is"
ImageMagick ImageMagick Rackham, Irma, Bianca, Snowy 6.9.9-35, 7.0.11-3 Derived Apache 2.0
jq jq Rackham, Irma, Bianca, Snowy 1.6 MIT
MariaDB MariaDB Rackham, Irma, Bianca, Snowy 10.1.29, 10.2.11 GPL v2
mbuffer mbuffer Rackham, Irma, Bianca, Snowy 20151002 GPL v3
MCL mcl Rackham, Irma, Bianca, Snowy 14-137 GPL v3
metaWRAP metaWRAP Rackham, Irma, Bianca, Snowy 1.3.2 MIT
Moses Moses Rackham, Bianca, Snowy, Miarka 4.0.0
Open Babel openbabel Rackham, Irma, Bianca, Snowy 3.1.1-gcc9.3.0 GPL v2
OpenBUGS OpenBUGS Rackham, Irma, Bianca, Snowy 3.2.3 GPL v2
p7zip p7zip Rackham, Irma, Bianca, Snowy 16.02 LGPLv2
Pandoc pandoc Rackham, Irma, Bianca, Snowy, Miarka 1.16.0.2, 2.2.3.2, 2.10.1, 2.17.1.1 GPL v2, GPL v3
Paraview paraview Rackham, Irma, Bianca, Snowy 5.6, 5.9.1 BSD
PostgreSQL PostgreSQL Rackham, Irma, Bianca, Snowy 10.3 PostgreSQL Licence
POV-Ray povray Rackham, Irma, Bianca, Snowy 3.7 AGPL v3
rclone rclone Rackham, Irma, Bianca, Snowy 1.56.2 MIT
ROOT ROOT Rackham, Irma, Bianca, Snowy 6.06.08, 6.20.04 LGPL v2.1
SAIGE SAIGE Rackham, Irma, Bianca, Snowy 0.42.1, 0.44.6.5 GPL v3
SCons SCons Rackham, Irma, Bianca, Snowy 2.5.0 misc free software
SWIG swig Rackham, Irma, Bianca, Snowy 3.0.7, 3.0.12 GPL v3 plus some "as is"
SQLite sqlite Rackham, Irma, Bianca, Snowy (system), 3.8.5, 3.11.1, 3.16.2, 3.24.0, 3.34.0 Public domain
Tcl-Tk Tcl-Tk Rackham, Irma, Bianca, Snowy 8.6.11 BSD-like
Tesseract tesseract Rackham, Irma, Bianca, Snowy 4.1.3 Apache 2.0
Texinfo texinfo Rackham, Irma, Bianca, Snowy 6.0, 6.5, 6.6, 6.8 GPL v3
TeX Live texlive Rackham, Irma, Bianca, Snowy, Miarka 2015, 2016, 2018, 2019, 2021, 2022-09-18 misc free software
tinyutils tinyutils Rackham, Irma, Bianca, Snowy 1.1, 1.2, 1.3, 1.4 GPLv2
tmux tmux Rackham, Irma, Bianca, Snowy 1.9a, 2.5, 3.1b Custom open-source AS IS
XZ Utils xz Rackham, Miarka, Bianca, Snowy 5.2.2, 5.2.6 Mixed
VIM vim Rackham, Irma, Bianca, Snowy 7.4-1941, 8.0-16, 8.0-1360, 8.1-1053, 8.2.3701 Custom
VSCodium VSCodium Rackham, Snowy, Bianca, Miarka 1.75.1.23040
vmtouch vmtouch Rackham, Irma, Bianca, Snowy 1.3.1-20200309-4b70a9f BSD
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, 2.1.0..3, 3.0.0..2, 3.1.0..6, 4.0.2, 4.0.3. 4.0.4 GPL
GNU parallel gnuparallel Rackham, Irma, Bianca, Snowy 20170122, 20180822 GPL
Libraries
Armadillo Armadillo Milou, Rackham, Irma, Bianca 20170510 Apache License 2.0
ARPACK-NG ARPACK-NG Milou, Rackham, Irma, Bianca 3.8.0 BSD Software License
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, 1.70.0_intel18.3_intelmpi18.3 Boost licence
bzip2 bzip2 Rackham, Bianca, Snowy, Miarka 1.0.6, 1.0.8 Custom open source "as is"
Cairo cairo Rackham, Irma, Bianca, Snowy 1.14.8, 1.14.12, 1.17.2, 1.17.4 GNU LGPL v2.1 or Mozilla Public Licence 1.1
deal.II deal.II Rackham, Irma, Bianca, Snowy 9.1.1-gcc built with foss/2019a toolchain, 9.1.1-intel built with intel/2019a toolchain GNU LGPL v2.1 or later
FFTW fftw Rackham, Irma, Bianca, Snowy 3.3.8 GPL
FreeType freetype Rackham, Irma, Bianca, Snowy 2.6, 2.7.1 BSD-like FreeType and GPL v2
GIFLIB giflib Rackham, Irma, Bianca, Snowy 5.1.4 Custom "as is"
GLPK glpk Rackham, Irma, Bianca, Snowy 4.63, 4.65 GPL
GMP GMP Rackham, Irma, Bianca, Snowy 6.2.1 LGPL v3; GPL v2
Gnu Scientific Library gsl Rackham, Bianca, Snowy, Miarka 1.16, 2.1, 2.3, 2.5, 2.6, 2.7 GPL
HDF4 hdf4 Rackham, Irma, Bianca, Snowy 4.2.11_gcc4.9.2, 4.2.14-gcc6.3.0 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, Bianca, Snowy, Miarka 7.45.0, 7.85.0 Custom open source "as is"
libHaru libharu Rackham, Irma, Bianca, Snowy 2.3.0 ZLIB/LIBPNG License
libicu libicu Rackham, Irma, Bianca, Snowy, Miarka 5.2-4 MIT and UCD and public domain
libTIFF libtiff Rackham, Irma, Bianca, Snowy 4.5.0 "As is"
libwebp libwebp Rackham, Irma, Bianca, Snowy 1.2.0 Google "as is" open source
lp_solve lpsolve Rackham, Irma, Bianca, Snowy 5.5.2.9 LGPL v2
MPC MPC Rackham, Irma, Snowy, Bianca 1.2.1 LGPL v3+
MPFR MPFR Rackham, Irma, Bianca, Snowy 4.1.0 LGPL v3+
NetCDF netcdf Rackham, Irma, Bianca, Snowy 4.7.1, 4.7.1-intel18.3 Custom open source "as is"
NLopt NLopt Rackham, Irma, Bianca, Snowy 2.6.1 MIT
OpenBLAS openblas Rackham, Irma, Bianca, Snowy 0.2.14a, 0.2.19, 0.2.19-singlethread, 0.2.20, 0.2.20-singlethread, 0.2.20-openmp, 0.3.15, 0.3.15-singlethread, 0.3.15-openmp BSD 3-clause
PCRE pcre Rackham, Irma, Bianca, Snowy 8.40 BSD 3-clause
PLplot PLplot Rackham, Irma, Bianca, Snowy 5.15.0, 5.15.0-old_wxWidgets LGPL v2
Poppler Poppler Rackham, Irma, Bianca, Snowy 0.54.0, 0.75.0 GPL v2
Protocol Buffers protobuf Rackham, Irma, Bianca, Snowy 3.11.4, 3.15.5, 3.15.5-gcc9.3.0 Google custom AS IS
pslib pslib Rackham, Irma, Bianca, Snowy 0.4.6 GPL, LGPL
Qhull Qhull Rackham, Irma, Bianca, Snowy 2019.1 Custom open source "as is"
readline readline Rackham, Irma, Bianca, Snowy, Miarka 6.2-11 GPL v3
scalapack scalapack Milou 1.8.0
SDSL SDSL Rackham, Irma, Bianca, Snowy, Miarka 2.1.1 GPL v3
Sodium libsodium Rackham, Irma, Bianca, Snowy 1.0.18-stable ISC
slurm-drmaa slurm-drmaa Rackham, Irma, Bianca, Snowy, Miarka 1.1.2-slurm19.05.8, 1.1.3-slurm19.05.08, 1.1.3-slurm21.08.2, 1.1.3-slurm21.08.8 GPL v3
sparsehash sparsehash Rackham, Irma, Bianca, Snowy, Miarka 2.0.2, 2.0.3, 2.0.4 BSD 3-clause
SuperLU SuperLU Rackham, Irma, Bianca, Snowy 5.2.1 Custom
SZIP szip Rackham, Irma, Bianca, Snowy 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, Snowy 2.2.26 Custom open source "as is"
wxWidgets wxWidgets Rackham, Irma, Bianca, Snowy 3.1.3-gtk2, 3.1.3-gtk3, 3.1.3-qt5 wxWindows Library Licence 3.1
Yeppp Yeppp Rackham, Irma, Bianca, Snowy 1.0.0 Custom open source "as is"
ZeroMQ libzmq Rackham, Irma, Bianca, Snowy 4.3.4 GPL v3
zlib zlib Rackham, Bianca, Snowy, Miarka 1.2.8, 1.2.11, 1.2.12 ZLIB License
zstd zstd Rackham, Irma, Bianca, Snowy, Miarka 1.5.2 GPL v2
Bioinformatics Alignment Module Cluster Version License
AGE AGE Rackham, Irma, Bianca, Snowy 0.4
ANFO anfo Rackham, Irma, Bianca, Snowy 0.98 GPL
ARAGORN aragorn Rackham, Irma, Bianca, Snowy 1.2.36, 1.2.38
Barrnap barrnap Rackham, Irma, Bianca, Snowy 0.2, 0.6, 0.8, 0.9 GPL v3
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 Rackham, Irma, Bianca, Snowy 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 Rackham, Irma, Bianca, Snowy 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+, 2.9.0+, 2.10.1+, 2.11.0+ 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 Rackham, Irma, Bianca, Snowy 0.7.12 GPL
bwa-mem2 bwa-mem2 Rackham, Irma, Bianca, Snowy, Miarka 2.2.1-20211213-edc703f MIT
bwa-meth bwa-meth Rackham, Irma, Bianca, Snowy 0.2.2 MIT
cactus cactus Rackham, Irma, Bianca, Snowy 1.0.0, 1.2.3 Custom open-source AS IS
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, Miarka 0.7.9, 0.7.12, 0.8.26, 0.9.10, 0.9.24, 0.9.26, 0.9.29,0.9.31, 2.0.4, 2.0.9, 2.0.14 GPL v3
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, 2017-11-15, 2018-02-12, 2018-07-04, 2021-03-08, 2021-12-17 Custom as-is
HAL hal Milou, Rackham 20151218, 20161130 open-source "as is" and others
HISAT2 HISAT2 Rackham, Irma, Bianca, Snowy 2.1.0, 2.2.1 GPL v3
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 Rackham, Irma, Bianca, Snowy, Miarka 1.1.1, 1.1.2, 1.1.4 BSD-style
Kalign Kalign Rackham, Irma, Bianca, Snowy 1.04, 2.04 GPL v2
LAST last Milou, Rackham, Irma, Bianca, Snowy 847, 963 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 Rackham, Irma, Bianca, Snowy 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 Rackham, Irma, Bianca, Snowy 20170914-82077ac Custom "As is"
Maq maq Rackham, Irma, Bianca, Snowy 0.7.1 GPL
MinCED minced Milou, Rackham, Irma, Bianca 0.2.0 GPL v3
Minimap2 minimap2 Rackham, Bianca, Snowy, Miarka 2.4, 2.14, 2.16, 2.17-r941, 2.18-r1015, 2.24-r1122 MIT
MMseqs2 MMseqs2 Rackham, Bianca, Snowy, Miarka 14-7e284 GPL v3
MOSAIK mosaik-aligner Rackham, Irma, Bianca, Snowy 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 Rackham, Irma, Bianca, Snowy 012109
MUMmer MUMmer Rackham, Irma, Bianca, Snowy 3.22, 3.23, 3.9.4alpha, 4.0.0beta2, 4.0.0rc1 Artistic License 2.0
MUSCLE muscle Rackham, Irma, Bianca, Snowy, Miarka 3.8.31, 3.8.1551, 5.1 Public domain, GPL v3
Nextflow Nextflow Rackham, Irma, Bianca, Snowy 0.17.3, 0.22.2, 0.26.0 GPLv3
NextGenMap NextGenMap Rackham, Irma, Bianca, Snowy 0.4.12, 0.5.4, 0.5.5 Artistic License 1.0
OMBlast OMBlast Rackham, Irma, Bianca, Snowy 1.0 unknown
OPTIMA optima Rackham, Irma, Bianca, Snowy f-1.3 GPL v2
pblat pblat Rackham, Irma, Bianca, Snowy, Miarka 2.0, 2.1, 2.5 Same as blat
pblat-cluster pblat-cluster Rackham, Irma, Bianca, Snowy, Miarka 0.1, 0.3, 1.0, 1.1 Same as blat
pfam_scan pfam_scan Rackham, Irma, Bianca, Snowy 1.3, 1.5, 1.6 GPL v3
pplacer pplacer Rackham, Irma, Bianca, Snowy 1.1.alpha19 GPL v3
PRANK prank Rackham, Irma, Bianca, Snowy 150803, 170427 GPL v2+
ProbCons ProbCons Rackham, Irma, Bianca, Snowy 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 Rackham, Bianca, Snowy, Miarka 2.1.4, 2.3.1, 2.4.0, 2.4.9, 2.4.13c 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, 2.7.9a

MIT, GPLv3 (prior to 2.7.2b)
T-Coffee T-Coffee Rackham, Irma, Bianca, Snowy 11.00.8cbe486, 13.39.0.d675aed GPL v2
TRF trf Rackham, Irma, Bianca, Snowy 4.07b, 4.09, 4.09.1 Gnu Affero GPL v3
tRNAscan-SE tRNAscan-SE Rackham, Irma, Bianca, Snowy, Miarka 1.3.1, 2.0.9 GPL v3
unimap unimap Rackham, Irma, Bianca, Snowy 0.1-r46-dirty MIT
Vmatch Vmatch Rackham, Irma, Bianca, Snowy 2.2.5, 2.3.0 Custom non-commercial
Vsearch vsearch Rackham, Irma, Bianca, Snowy 2.3.2, 2.4.3, 2.5.2, 2.14.1, 2.18.0 GPL v3 or BSD 2-clause
Wise2 wise2 Rackham, Irma, Bianca, Snowy 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, 3.3.3, 3.3.3-CGP Artistic License
BRAKER braker Rackham, Irma, Bianca, Snowy 2.1.1_Perl5.24.1, 2.1.5, 2.1.5-20200826-cf958ec, 2.1.5-20210115-e98b812, 2.1.6 Artistic License
CEGMA cegma Rackham, Irma, Bianca, Snowy 2.5
Delly delly Rackham, Irma/Miarka, Bianca, Snowy 0.7.6, 0.7.7, 1.1.6 GPL v3, BSD
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, 1.7.1 Custom "AS IS"
GUSHR GUSHR Rackham, Irma, Bianca, Snowy 1.0.0 GPL v3
HaMStR HaMStR Rackham, Irma, Bianca, Snowy 13.2.3 GNU GPL 3
HOMER HOMER Rackham, Irma, Bianca, Snowy 4.10, 4.11 GPL v3
InterProScan InterProScan Rackham, Irma, Bianca, Snowy 5.30-69.0, 5.52-86.0 Misc
libBigWig libBigWig Rackham, Irma, Bianca, Snowy 0.4.4 MIT
MakeHub MakeHub Rackham, Irma, Bianca, Snowy 1.0.5-1ecd6bb GPL v3
MAKER maker Rackham, Irma, Bianca, Snowy 2.31.9, 2.31.10, 3.01.1-beta, 3.01.2-beta, 3.01.2-beta-mpi, 3.01.04 GPL
Oncotator oncotator Rackham, Irma, Bianca, Snowy 1.9.9.0 BROAD INSTITUTE SOFTWARE LICENSE AGREEMENT FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
ORFfinder ORFfinder Rackham, Irma, Bianca, Snowy, Miarka 0.4.3 Public Domain
Phobius Phobius Rackham, Irma, Bianca, Snowy 1.01 Private study, education and non-profit research only
ProtHint ProtHint Rackham, Irma, Bianca, Snowy 2.4.0, 2.5.0, 2.6.0 GeneMark license 
Scipio Scipio Rackham, Irma, Bianca, Snowy 1.4.1 Custom non-commercial
SignalP SignalP Rackham, Irma, Bianca, Snowy 4.1c, 4.1f, 5.0b 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
TargetP TargetP Rackham, Irma, Bianca, Snowy 2.0 Custom academic 'AS IS'
TMHMM tmhmm Rackham, Irma, Bianca, Snowy 2.0c Custom academic as-is
TransDecoder TransDecoder Rackham, Irma, Bianca, Snowy 5.0.1, 5.3.0, 5.5.0 Custom open-source 'AS IS'
Trinotate trinotate Rackham, Irma, Bianca, Snowy 3.0.2, 3.1.1, 3.2.2 Custom open-source 'AS IS'
TSEBRA TSEBRA Rackham, Irma, Bianca, Snowy 1.0.2-20210716-1f167ad, 1.0.3-20211126-336c380 Artistic License 2.0
VIBRANT VIBRANT Rackham, Irma, Bianca, Snowy 1.2.1 GNU General Public License
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
ARCS ARCS Rackham, Irma, Bianca, Snowy 1.0.6, 1.1.1 GPL v3
ArrowGrid ArrowGrid Rackham, Irma, Bianca, Snowy 20191022-9759eb1 Public Domain
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, 2.0, 2.2 GPL v2 and others for subcomponents
DBG2OLC DBG2OLC Milou 20151208
DISCOVAR de novo DISCOVARdenovo Milou 51885 Custom "as is"
FALCON FALCON Rackham, Irma, Bianca, Snowy 0.3.0, 0.4.1, 2018.31.08-03.06 Clear BSD
FALCON-integrate FALCON-integrate Rackham, Irma, Bianca, Snowy 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, 2.9 BSD 3-clause
GAA GAA Rackham, Irma, Bianca, Snowy 1.1 GPL v2+
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
IRMA IRMA Rackham, Bianca, Snowy, Miarka 1.0.3 GPL v3
Kourami kourami Rackham, Irma, Bianca, Snowy 0.9.6 BSD 3
LINKS LINKS Rackham, Irma, Bianca, Snowy 1.8.7 GPL v3
LoRDEC LoRDEC Rackham, Irma, Bianca, Snowy 0.9 CeCILL 2.1
MaSuRCA MaSuRCA Rackham, Irma, Bianca, Snowy 3.2.2, 3.2.3, 3.3.5, 3.4.2, 4.0.2 GPL v3
MEGAHIT megahit Milou, Rackham, Irma, Bianca 1.0.3, 1.1.2, 2.0.4 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
NextDenovo NextDenovo Rackham, Irma, Bianca, Snowy 2.4.0, 2.5.0 GNU
Oases oases Milou 0.2.08 GPL
pbbam pbbam Rackham, Irma, Bianca, Snowy 1.6.0 PacBio open source license
PBSuite (contains PBJelly and PBHoney) PBSuite Milou, Rackham, Irma, Bianca 15.8.24 Custom redistributable "as is"
Pilon Pilon Milou, Snowy, Rackham, Irma, Bianca 1.17, 1.22, 1.24 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
quickmerge quickmerge Rackham, Irma, Bianca, Snowy 0.3-9233726 GPL v3
RACA (Reference-Assisted Chromosome Assembly) RACA Milou 0.9.1.1
Racon Racon Rackham, Irma, Bianca, Snowy 1.4.21 MIT
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-20190314-de_novo-42e8edf (development only), 0.14a-20190313-d11d32b, 0.14a-20190509-ffae69e GPL v2
satsuma2 satsuma2 Milou, Rackham, Irma, Bianca

2016-12-07
37c5f38-20200304

LGPL v3+
SGA SGA Rackham, Irma, Bianca, Snowy 0.10.14

GPL v3

Shasta Shasta Rackham, Irma, Bianca, Snowy 0.7.0

MIT

SMARTdenovo SMARTdenovo Rackham, Irma, Bianca, Snowy 20180219-5cc1356, 20210224-8488de9 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, 3.14.1, 3.15.3 GPL v3,GPLv2(3.14.1)
StringTie StringTie Rackham, Irma, BIanca, Snowy 1.2.0, 1.3.3, 2.1.4 MIT
Tigmint tigmint Rackham, Irma, Bianca, Snowy 1.1.2 GPL v3
Trans-ABySS transabyss Milou 1.5.3 BCCA "As Is"
Trinity trinity Rackham, Irma, Bianca, Snowy 2014-07-17, 2.4.0, 2.9.1, 2.11.0, 2.13.2 Custom 'AS IS'
Unicycler Unicycler Rackham, Irma, Bianca, Snowy 0.4.8, 0.5.0 GPL v3
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
ABCtoolbox ABCtoolbox Rackham, Bianca, Snowy, Miarka 20131120
abricate abricate Rackham, Bianca, Snowy, Miarka 0.8.7, 1.0.1-20200512-955d402 GPL v2
AdapterRemoval AdapterRemoval Milou, Rackham, Irma, Bianca 2.1.7, 2.2.2 GPL v3
AdmixTools AdmixTools Rackham, Irma, Bianca, Snowy 20160803, 5.0-20170312, 5.0-20171024, 7.0.1 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 Rackham, Irma, Bianca, Snowy 0.917, 0.917-g6522d3e, 0.921, 0.933 Open source
ANTs ANTs Rackham, Irma, Bianca, Snowy 2.3.1 Custom open-source "as is"
any2fasta any2fasta Rackham, Bianca, Snowy, Miarka 0.4.2 GPL v3
Arlequin Arlequin Rackham, Irma, Bianca, Snowy, Miarka 3.5.2.2
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
bam2fastx bam2fastx Rackham, Irma, Bianca, Snowy 1.3.0-80dbf79 BSD 3-clause
BamBam bambam Rackham, Irma, Bianca, Snowy 1.4 MIT
Bamtools bamtools Milou, Rackham, Irma, Bianca 2.3.0, 2.5.1 MIT
Bamsurgeon Bamsurgeon Rackham, Irma, Bianca, Snowy 1.3 MIT License
BCFtools bcftools Rackham, Irma, Bianca, Snowy 1.2, 1.3.1, 1.5, 1.6, 1.8, 1.9, 1.9-develop, 1.10, 1.12, 1.14 MIT/Expat or GPL v3
BclConverter Bclconverter Rackham, Irma, Bianca, Snowy, Miarka 1.7.1, 3.9.3 Custom Illumina
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
BioBakery
(Metapackage that includes MetaPhlAn, PhyloPhlan, KneadData and HUMAnN)
BioBakery Rackham, Irma, Bianca, Snowy 3.0 MIT
BioBloom Tools BioBloomTools Rackham, Irma, Bianca, Snowy, Miarka 2.3.3-20210218-151b0c0 GPL v3
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 1.68 (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), 1.76-py3 (python/3.7.2) 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, 0.22.3, 0.23.1 GPL
BOLT-LMM BOLT-LMM Rackham, Irma, Bianca, Snowy 2.3.5 GPL v3
bonito (requires GPU) bonito Bianca, Snowy 0.3.8 Oxford Nanopore Public License 1.0
BraCeR BraCeR Rackham, Irma, Bianca, Snowy 2019_10_03_22e49cb Apache 2.0
BreakDancer breakdancer Rackham, Irma, Bianca, Snowy 1.4.5-4e44b43 GPL 3
BUSCO (with all lineage sets) BUSCO Rackham, Irma, Bianca, Snowy 1.22, 2.0.1, 3.0.2b, 4.1.4, 4.0.0, 5.2.2 GPL v3+
CAMMiQ CAMMiQ Rackham, Irma, Bianca, Snowy, Miarka 20211015-6142150 MIT for CAMMiQ but uses CPLEX
CD-Hit aka cdhit cd-hit Rackham, Irma, Bianca, Snowy 3.1.1, 4.6.1, 4.6.4, 4.6.8-2017-1208, 4.8.1 GPL v2
cdbfasta cdbfasta Rackham, Irma, Bianca, Snowy 0.99, 1.00 Artistic 2.0
Cell Profiler cellprofiler Milou 2.1.0
Cell Ranger ATAC cellranger-ATAC Rackham, Irma, Bianca, Snowy 1.2.0 Misc non-commercial
Centrifuge Centrifuge Rackham, Irma, Bianca 1.0.4-beta GPL v3
CGAT CGAT Rackham, Irma, Bianca, Snowy 0.3.3 "As is" 
CheckM CheckM Rackham, Irma, Bianca, Snowy 1.0.11, 1.0.12, 1.1.3 GPL v3
CIRCexplorer CIRCexplorer Rackham, Irma, Bianca 1.1.10
CITE-seq-Count CITE-seq-Count Rackham, Irma, Bianca, Snowy 1.4.3 MIT
CleaveLand4 CleaveLand4 Milou, Rackham, Irma, Bianca 4.3 GPL v3
Conterminator Conterminator Rackham, Irma, Bianca, Snowy 20200601-570993b
cnD cnD Milou 1.3 GPL 3
CNV-seq CNV-seq Milou 20140812 Misc open source
CNVnator CNVnator Rackham, Irma, Bianca, Snowy 0.3.3, 0.4.1-20200707-c73786d Custom AS IS
CONCOCT CONCOCT Rackham, Irma, Bianca, Snowy 0.5.0, 1.1.0 FreeBSD
Corset Corset Milou, Rackham, Irma, Bianca 1.04, 1.07 GPL v3
CRAM Tools cramtools Milou, Rackham, Irma, Bianca 2.0, 3.0
DANPOS DANPOS Rackham, Snowy, Irma, Bianca 2.2.2, 3.1.1
DATES DATES Rackham, Irma, Bianca, Snowy 753
datamash datamash Rackham, Irma, Bianca, Snowy 1.8
deepTools deepTools Rackham, Irma, Bianca, Snowy 2.2.3, 2.3.1, 2.4.3, 2.5.1, 3.1.0, 3.3.2 BSD and MIT
DelGet DelGet Rackham, Irma, Bianca, Snowy 5.4
DosageConvertor DosageConvertor rackham, irma, bianca, snowy 1.0.4 custom
DWGSIM DWGSIM Milou, Rackham, Irma, Bianca 0.1.11-6e9a361 GPL v2
EDirect EDirect Rackham, Irma, Bianca, Snowy 15.1 Public Domain
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,rackham, irma, bianca, snowy 87(Milou),94 Modified Apache, Apache 2.0
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
FastANI FastANI Rackham, Irma, Bianca, Snowy 1.2 Apache 2.0
fastNGSadmix fastNGSadmix Milou, Rackham, Irma, Bianca 20170825-099ab7f
fastp fastp Rackham, Irma, Bianca, Snowy, Miarka 0.20.0, 0.23.1, 0.23.2 MIT
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, 0.11.9 GPL
fastq_screen fastq_screen Rackham, Irma, Bianca, Snowy 0.5.1, 0.9.2, 0.11.1, 0.15.2 GPL
fastqtk fastqtk Rackham, Irma, Bianca, Snowy 0.27 MIT
fastsimcoal fastsimcoal Rackham, Bianca, Snowy, Miarka 2.7.9, 2.7.93
FASTX Fastx Rackham, Irma, Bianca, Snowy 0.0.14 AGPLv3
fcGENE fcGENE Rackham, Irma, Bianca, Snowy 1.0.7 GPL
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 Rackham, Irma, Bianca, Snowy 0.8.9, 0.9.4, 0.9.4_2012-04-16, 0.9.8, 0.9.21, 1.0.2, 1.1.0, 1.3.2 Custom open-source "as-is"
FusionCatcher FusionCatcher Rackham, Irma, Bianca, Snowy, Miarka 1.00, 1.10, 1.33 GPL
GAAS GAAS Rackham, Irma, Bianca, Snowy, Miarka 1.2.0 GPL v3
GCTA gcta Rackham, Irma, Bianca, Snowy 1.26.0, 1.93.2beta, 1.94.1 MIT
GEM GEM Rackham, Irma, Bianca, Snowy 2.7, 3.4 "Research only"
GEMMA GEMMA Rackham, Irma, Bianca, Snowy 0.98.1 GPL3
GeneMark GeneMark Rackham, Bianca, Snowy, Miarka 2.3-es, 4.32-es, 4.33-es, 4.33-es_Perl5.24.1, 4.38-es, 4.57-es, 4.62-es, 4.68-es, 4.69-es GeneMark licence
Genepop Genepop Rackham, Irma, Bianca, Snowy 4.7 CeCILL (GPL compatible)
GenomeTools GenomeTools Rackham, Irma, Bianca, Snowy 1.5.9, 1.6.1 ISC
GERP++ GERP++ Rackham, Irma, Bianca, Snowy 20110522 GPL v3+
gffread gffread Rackham, Irma, Bianca,Snowy 0.12.6 MIT
GTOOL GTOOL Milou 0.7.5 "As is" open source
Guppy Guppy Rackham (-cpu only),  Bianca, Snowy, Miarka

5.0.16-cpu, 5.0.16-gpu, 6.3.7-cpu, 6.3.7-gpu

Custom
gvcftools gvcftools Milou, Rackham, Irma, Bianca 0.16.2, 0.17.0 Various "As Is" open source
HESS HESS Rackham, Irma, Bianca, Snowy 0.5.4-beta GPL v3
HiCExplorer HiCExplore Rackham, Irma, Bianca, Snowy 2.2-beta GPL v3
HiCUP HiCUP Rackham, Irma, Bianca, Snowy 0.7.2 GPL v3 or later
HTSlib htslib Rackham, Irma, Bianca, Snowy 1.3, 1.3.2, 1.4, 1.5, 1.6, 1.8, 1.9, 1.10, 1.12, 1.14 MIT/Expat and modified 3-clause BSD
HTSeq htseq Rackham, Bianca, Snowy, Miarka 0.9.1, 0.12.4, 2.0.2 GPL v3
HUMAnN HUMAnN Rackham, Irma, Bianca, Snowy 3.0 MIT
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 Rackham, Irma, Bianca, Snowy 1.1.11, 1.1.12, 2.2.6, 2.3.0 GPL
kaiju kaiju Rackham, Irma, Bianca, Snowy 1.6.2, 1.7.2 GPL v3
kallisto kallisto Rackham, Irma, Bianca, Snowy 0.42.4, 0.43.0, 0.43.1, 0.45.1, 0.46.2 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
KING KING Snowy, Bianca, Rackham, Miarka 2.2.9
KmerGenie KmerGenie Milou, Rackham, Irma, Bianca 1.6741, 1.7039 Other
KneadData KneadData Rackham, Irma, Bianca, Snowy 0.10.0 MIT
Kraken Kraken Rackham, Irma, Bianca, Snowy 0.10.5-beta, 1.0, 1.1-352e780, 1.1.1, 1.1.1-20210927-375654f GPL v3
Kraken2 Kraken2 Rackham, Irma, Bianca, Snowy, Miarka 2.0.7-beta-bc14b13, 2.0.8-beta, 2.1.1, 2.1.2-20211210-4f648f5 MIT
KrakenHLL KrakenHLL Rackham, Irma, Bianca 0.4.9
KrakenUniq KrakenUniq Rackham, Bianca, Snowy, Miarka 0.6, 1.0.0, 1.0.1 GPLv3, MIT
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
LDpred LDpred Rackham, Irma, Bianca, Snowy 0.9.9, 1.0.8, 1.0.10, 1.0.11 MIT
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 Rackham, Irma, Bianca, Snowy 0.2.13-97cf18c, 0.2.13-213a417, 0.3.0 MIT
MACS MACS Rackham, Irma, Bianca, Snowy 2.1.0, 2.1.2, 2.2.6, 3.0.0a6 BSD 3-clause
MACE MACE Milou 1.2
MAGeCK MAGeCK Rackham, Irma, Bianca, Snowy 0.5.6, 0.5.9.4 BSD 3-clause
MAGeCK2 MAGeCK2 Rackham, Miarka, Bianca, Snowy 20211209-435eacd 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
MAPGD MAPGD Milou, Rackham, Irma, Bianca, Snowy 0.4.40 GPL
matrix2png matrix2png Milou 1.2.1 Apache
MaxBin MaxBin Rackham, Bianca, Irma, Snowy 2.2.5, 2.2.7 BSD
medaka medaka Rackham, Bianca, Irma, Snowy 0.7.1, 1.4.3 MPL 2.0
Meerkat Meerkat Milou 0.189 Misc non-commercial open source
Megalodon Megalodon Rackham, Bianca, Snowy 2.5.0
mergeSVcallers mergeSVcallers Milou, Rackham, Irma, Bianca 161006-23533ef
MetaBAT MetaBat Milou, Rackham, Irma, Bianca 0.26.3, 2.12.1 BSD-like
MetaCRAST MetaCRAST Rackham, Irma, Bianca, Snowy 20200310-ed82df4
METAL METAL Rackham, Irma, Bianca, Snowy 2011-03-25 open source
MetaSV MetaSV Milou, Rackham, Irma, Bianca 0.5.4 BSD 2-clause
Metaxa2 Metaxa2 Rackham, Irma, Bianca, Snowy 2.1.3, 2.2 GPL v3
MethPipe MethPipe Rackham, Irma, Bianca, Snowy 3.4.3, 4.1.1 GPL v3+
MethylDackel MethylDackel Rackham, Irma, Bianca, Snowy 0.2.1, 0.5.1 MIT
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
mosdepth mosdepth Rackham, Snowy, Bianca 0.3.3
Mothur Mothur Rackham, Irma, Bianca, Snowy 1.40.5, 1.41.0 GPL v3
ms ms Rackham, Irma, Bianca, Snowy 20071014 open source
MSMC msmc Rackham, Irma, Bianca, Snowy 0.1.0, 1.1.0 GPL v3
MultiQC MultiQC Rackham, Irma, Bianca, Snowy, Miarka 0.6, 0.7, 0.8, 0.9, 1.0, 1.2, 1.3, 1.5, 1.6, 1.7, 1.8, 1.9, 1.10, 1.10.1, 1.11, 1.12 MIT
MuSIC2 music2 Rackham,Irma,Bianca, Snowy 0.2 MIT
MuTect mutect Milou, Rackham, Irma, Bianca 1.1.5 Other
NanoComp NanoComp Rackham, Irma, Bianca, Snowy 1.9.2 GPL v3
NanoPlot NanoPlot Rackham, Irma, Bianca, Snowy 1.33.1 GPL v3
NeEstimator NeEstimator Rackham, Irma, Bianca, Snowy 2.1 AS IS
NeuSomatic NeuSomatic Rackham, Irma, Bianca, Snowy 0.2.1 Creative Commons Public License
NGSadmix NGSadmix Rackham, Irma, Bianca, Snowy 32
ngsF-HMM ngsF-HMM Rackham, Irma, Bianca, Snowy, Miarka 20200720-2df9690 GPL-3.0
ngsLD ngsLD Rackham, Irma, Bianca, Snowy, Miarka 1.1.1 GPL v2
ngsplot ngsplot Rackham, Irma, Bianca, Snowy 2.61, 2.63 GPL v2
NgsRelate NgsRelate Rackham, Irma, Bianca, Snowy 2.0 GPL v2
NGSrich ngsrich Rackham, Irma, Bianca, Snowy 0.7.8
NGSUtils NGSUtils Rackham, irma, Bianca, Snowy 0.5.9 Custom open source "as is"
nibabel nibabel Rackham, Irma, Bianca, Snowy 2.3.3 MIT + BSD
NPStat NPStat Rackham, Irma, Bianca, Snowy 1 GPL version 3
nseg nseg Rackham, Irma, Bianca, Snowy 1.0.1 Public Domain
octopus octopus Rackham, Miarka, Bianca, Snowy 17a597d-20220708 MIT
ont_fast5_api ont_fast5_api Rackham, Irma, Bianca, Snowy 3.1.6 Mozilla Public LIcense 2.0
OpenMS OpenMS Milou 2.0.0 BSD + other
OptiType OptiType Milou, Rackham, Irma, Bianca 1.3.1 BSD 3-Clause
OrthoMCL OrthoMCL Rackham, Irma, Bianca, Snowy 2.0.9
PCAngsd PCAngsd Rackham, Miarka, Bianca, Snowy 0.982, 1.11 GPL v3
PEAR pear Milou, Rackham, Irma, Bianca 0.9.5, 0.9.10 CC
PennCNV PennCNV Milou 20151014 Public domain
phantompeakqualtools phantompeakqualtools Milou, Rackham, Irma, Bianca 1.1 MIT
phASER phaser Snowy, Rackham, Irma, Bianca 20210423-5d4926d GNU
PhyloPhlAn

phylophlan

PhyloPhlan

Snowy, Rackham, Irma, Bianca

0.99

3.0.2

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, 2.23.4 MIT
PileOMeth (continued by MethylDackel) PileOMeth Milou 0.1.13
Pindel pindel Milou 0.2.4w GPL 3
pixy pixy Rackham, Irma, Bianca, Snowy 1.2.5.beta1 MIT License
pizzly pizzly Rackham, Irma, Bianca, Snowy 0.37.3 BSD 2-clause
PLINK plink Rackham, Irma, Bianca, Snowy 1.07, 1.90b3n, 1.90b4.9 GPL v3
PLINK2 plink2 Rackham, Miarka, Bianca, Snowy 2.00-alpha-2-20180704, 2.00-alpha-2-20190429, 2.00-alpha-2.3-20200124, 2.00-alpha-3.7-20221024 GPL v3
PLINK/SEQ plinkseq Rackham, Irma, Bianca, Snowy 0.08, 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
PRSice PRSice rackham, irma, bianca, snowy 2.2.11.b GPL3
PSMC psmc Rackham, Irma, Bianca, Snowy 0.6.5-r67-e5f7df5 MIT
pyGenomeTracks pyGenomeTracks Rackham, Irma, Bianca, Snowy 2.1 GPL v3
PySam pysam Rackham, Irma, Bianca, Snowy 0.7.7 (python 2.7.6), 0.7.7-py3 (python 3.3.1), 0.8.3 (python 2.7.6), 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, 0.15.3-python3.6.8, 0.15.3-python3.7.2, 0.17.0-python3.9.5 MIT
QCTOOL qctool Rackham, Irma, Bianca, Snowy 1.4, 2.0.1, 2.0.6 "As is" open source
QuantiSNP QuantiSNP Milou 2.2
QUAST quast Milou, Rackham, Irma, Bianca 2.2, 2.3, 3.2, 4.5.4, 5.0.2
QuorUM QuorUM Rackham, Irma, Bianca, Snowy 1.0.0 GPL v3
RAisD RAisD Rackham, Irma, Bianca, Snowy 2.9 GPL v2
Rcorrector Rcorrector Rackham, Irma, Bianca, Snowy 1.0.4 GPL v3
RDP Classifier rdp-classifier Rackham, Irma, Bianca, Snowy 2.2, 2.4
RDXplorer RDXplorer Rackham, Irma, Bianca, Snowy 3.2 open source
RECON RECON Rackham, Irma, Bianca, Snowy 1.08 GPL
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, 4.1.0 open source
RepeatModeler RepeatModeler Rackham, Irma, Bianca, Snowy 1.0.8_RM4.0.7, 1.0.11 open source
RepeatScout RepeatScout Rackham, Irma, Bianca, Snowy 1.0.5, 1.0.6 open source
RGT RGT Rackham, Irma, Bianca, Snowy 0.11.6 GPL v3+
rMATS-turbo rMATS-turbo Rackham, Irma, Bianca, Snowy 4.1.2 FreeBSD
Roary Roary Rackham, Irma, Bianca, Snowy 3.6.2, 3.12.0, 3.13.0 GPL v3
RSEM rsem Rackham, Irma, Bianca, Snowy 1.3.1, 1.3.3 GPL v3
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
RVTESTS rvtests Rackham, Irma, Bianca, Snowy 2.0.6
SACRA SACRA Rackham, Irma, Bianca, Snowy 1.0.0 MIT 3
Sailfish Sailfish Rackham, Irma, Bianca, Snowy 0.8.0 GPL v3+
Salmon Salmon Rackham, Irma, Bianca, Snowy 0.8.2, 0.9.1, 0.11.2, 1.1.0, 1.4.0, 1.6.0 GPL v3+
SalmonTE SalmonTE Rackham, Irma, Bianca, Snowy 20180926
sambamba sambamba Rackham, Irma, Bianca, Snowy 0.5.9, 0.6.6, 0.7.1 GPL v2+
samblaster samblaster Rackham, Irma, Bianca, Snowy 0.1.22, 0.1.24 MIT
samplefq samplefq Rackham, Irma, Bianca, Snowy 0.2 GPL v3
samstat samstat Rackham, Irma, Bianca, Snowy 1.5.1 GPL v3
SAMtools samtools Rackham, Irma, Bianca, Snowy 0.1.19, 1.1, 1.2, 1.3, 1.4, 1.5, 1.5_debug, 1.6, 1.8, 1.9, 1.10, 1.12, 1.14 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 Rackham, Irma, Bianca, Snowy 20160424, 20200706-597c6bc GPL v3
SCORE-Seq SCORE-Seq Milou 5.3
Selscan selscan Milou, Rackham, Irma, Bianca 1.1.0, 1.3.0 GPL v3
SeqAn SeqAn Milou, Rackham, Irma, Bianca 1.4.2 Other open-source
SeqKit SeqKit Rackham, Irma, Bianca, Snowy 0.15.0 MIT License
seqMINER seqMINER Milou 1.3.3e
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
seqtk seqtk Milou, Rackham, Irma, Bianca 1.0-r31, 1.0-r57, 1.0-r68e, 1.2-r101 MIT
SeqTools SeqTools Milou, Rackham, Irma, Bianca 4.20, 4.44.1 Apache 2.0
SHAPEIT SHAPEIT Rackham, Irma, Bianca, Snowy v2.r837, v2.r904, v3.r884.2, v4.1.3 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 2.6, 3.2.1, 3.3.2, 3.6, 4.0.1 GPL v3
SMC++ SMC++ Rackham, Irma, Bianca, Snowy 1.15.2, 1.15.4 GPL v3
snap snap Milou, Rackham, Irma, Bianca 2013-02-16, 2013-11-29 GPL
SNeP SNeP Rackham, Snowy, Irma, Bianca 1.1 AS IS
Sniffles Sniffles Rackham, Snowy, Irma, Bianca 1.0.10, 1.0.12-201218-4ff6ecb MIT license
snippy snippy Rackham, Irma, Bianca, Snowy 4.0, 4.0.5, 4.6.0 GPL 2.0
SNP2HLA SNP2HLA Rackham, Irma, Bianca, Snowy 1.0.3
snpAD snpAD Rackham, Irma, Bianca, Snowy 0.3.0, 0.3.4 open source
SNPTEST SNPTEST Rackham, Irma, Bianca, Snowy 2.5.2, 2.5.5 "As is" open source
SomaticSeq SomaticSeq Milou 1.2.1 Other
Space Ranger (Chromium 10X) spaceranger Rackham, Irma, Bianca, Snowy 1.0.0, 1.2.0 other
SPP SPP Rackham, Irma, Bianca, Snowy 1.11 GPL v2
SQuIRE SQuIRE Rackham, Irma, Bianca, Snowy, Miarka 885bf4d-20190301 GPL v3
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, 3.0.0 Public domain
Stacks Stacks Rackham, Irma, Bianca, Snowy 1.48, 2.0Beta9, 2.0b, 2.2, 2.41, 2.53 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 Rackham, Irma, Bianca, Snowhy 1.5.0, 1.5.1, 1.5.2, 2.0.0 GPL v3
SvABA SvABA Rackham, Irma, Bianca, Snowy 1.1.3-20201112-0f60e36 GPL v3
SVDetect SVDetect Milou 0.8b
SVMerge SVMerge Milou 1.2r37 Open source "as is"
svprops svprops Milou, Rackham, Irma, Bianca 20171020-ebf6762 GPL v3+
SweeD SweeD Milou, Rackham, Irma, Bianca 4.0.0 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
Tombo Tombo Rackham, Irma, Bianca, Snowy 1.5.1 Mozilla Public License 2.0
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, 0.39 GPL
TSC TSC Milou, Rackham, Irma, Bianca 1.2
UCSC Bioinformatics Utilities ucsc-utilities Rackham, Irma, Bianca, Snowy v287, v334, v345, v398, v421 Non-commercial
UMI-tools umi_tools Rackham, Irma, Bianca, Snowy 0.5.3, 0.5.4, 1.0.0 MIT
usearch (32-bit version); see vsearch for similar 64-bit capable tool usearch Rackham, Irma, Bianca, Snowy 5.2.236, 5.2.32, 6.1.544, 7.0.1090, 8.1.1861, 9.2.64, 11.0.667 Other
VarDictJava VarDictJava Rackham, Irma, Bianca, Miarka 1.4.5, 1.8.3 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
vawk vawk Rackham, Irma, Bianca, Snowy 0.0.1 MIT
VCFaid VCFaid Milou, Rackham, Irma, Bianca 20170616-f0732ae GPL v3
vcflib vcflib Rackham, Irma, Bianca, Snowy 2017-04-04, 1.0.1 MIT
Variant Effect Predictor from Ensembl Tools vep Milou, Rackham, Irma, Bianca 82, 84, 86, 87, 89, 91, 92 Modified Apache
VESPA VESPA Milou, Rackham, Irma, Bianca 1.0.1 GPLv3
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 the same module Rackham, Irma, Bianca, Snowy 1.8.4, 2.1.8, 2.2.5, 2.3.1, 2.4.17 MIT
velocyto velocyto Rackham, Irma, Bianca, Snowy 0.17.17 BSD 2-Clause
vt vt Milou, Rackham, Irma, Bianca 0.5772 MIT
XP-CLR XP-CLR Miarka, Rackham, Irma, Bianca 1.1.2 MIT
Bioinformatics Phylogeny Module Cluster Version License
beagle-lib beagle Rackham, Irma, Bianca, Snowy 2.1.2, 3.1.2 GPL
BEAST beast Milou, Rackham, Irma, Bianca 1.7.5, 1.8.1, 1.8.4 GPL
BEAST2 beast2 Rackham, Irma, Bianca, Snowy 2.1.2, 2.3.1, 2.4.0, 2.4.8, 2.6.2, 2.6.3 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
FastME FastME Rackham, Irma, Bianca, Snowy 2.1.6.2 GPL v3
FastML FastML Rackham, Irma, Bianca, Snowy 3.1, 3.11 GPL v2+
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 1.5.3-omp, 1.5.4-omp-mpi, 1.6.5-omp-mpi, 1.6.10-omp-mpi, 1.6.12-omp-mpi, 2.0-rc2-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, 6.20.17 Personal academic
MetaPhlAn2 metaphlan2 Rackham, Irma, Bianca, Snowy 2.0
MetaPhlAn3 MetaPhlAn3 Rackham, Irma, Bianca, Snowy 3.0.8 MIT license
MrBayes mrbayes Milou, Rackham, Irma, Bianca, Snowy 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), 3.2.7a with gcc 8.3.0 (mpi, gpu) Public domain
NEXUS Class Library ncl Milou, Rackham, Irma, Bianca 2.1.21-dev Simplified BSD
PAML paml Snowy, Rackham, Irma, Bianca 4.6, 4.9e, 4.9j Other
PathPhynder pathPhynder Rackham, Bianca, Snowy, Miarka 2020-12-19-b8532c0, 1.a-20221011-a407a97 MIT
Phast phast Rackham, Irma, Bianca, Snowy 1.4, 1.5, 1.6 BSD
PhyloBayes phylobayes Rackham, Irma, Bianca, Snowy 4.1c
PhyloBayes MPI phylobayesmpi Rackham, Irma, Bianca, Snowy 1.8, 1.8b GPL v2
PhyML PhyML Rackham, Irma, Bianca, Snowy 3.1, 3.3.20190321 GPL v3
Phynder phynder Rackham, Bianca, Snowy, Miarka 2020-08-17-48b184f MIT
Phyutility phyutility Rackham, Irma, Bianca, Snowy 2.7.3
RAxML raxml Rackham, Irma, Bianca, Snowy 7.3.0, 8.2.10-gcc, 8.2.10-gcc-mpi, 8.2.12-gcc, 8.2.12-gcc-mpi GPL v3
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, 1.1.0, 1.1.0-mpi GNU Affero GPL v3.0
Yleaf Yleaf Rackham, Irma, Bianca, Snowy 20180326, 2.0
Bioinformatics Pipelines Module Cluster Version License
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, 3.1, 4.0 MIT
Cytoscape Cytoscape Rackham, Miarka, Bianca, Snowy 3.9.1 LGPL 2.1
DeepVariant DeepVariant Rackham, Irma, Bianca, Snowy 0.8.0 BSD-3
dentist dentist Rackham, Miarka, Bianca, Snowy 4.0.0 MIT
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
Juicer Juicer Rackham, Miarka, Bianca, Snowy 1.6, 2.0 MIT
McClintock McClintock Rackham, Miarka, Bianca, Snowy 2.0.0
MIP mip Rackham, Irma, Bianca, Snowy 6.0.0 MIT
Nextflow Nextflow Rackham, Irma, Bianca, Snowy 18.10.1
nf-core nf-core Rackham, Irma, Bianca, Snowy 1.12.1, 1.14, 2.1
nf-core-pipelines nf-core-pipelines Rackham, Irma, Bianca, Snowy latest
Qiime Qiime Rackham, Snowy 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 Rackham, Irma, Bianca, Snowy 3.10.1, 4.5.0, 5.2.3, 5.4.5, 5.10.0, 5.13.0, 5.17.0, 5.26.1, 5.30.1, 6.9.1, 7.8.5, 7.18.1, 7.18.2, 7.25.0
Tophat tophat Rackham, Irma, Bianca, Snowy 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 Rackham, Irma, Bianca, Snowy 1.8.4, 2.15.0, 2.16.0, 2.17.1, 2.20.0
BEDOPS BEDOPS Rackham, Irma, Bianca, Snowy 2.4.3, 2.4.28, 2.4.39 GPL v2
BEDTools BEDTools Rackham, Irma, Bianca, Snowy 2.21.0, 2.23.0, 2.25.0, 2.26.0, 2.27.1, 2.29.2 GPL
BioScope BioScope Rackham, Irma, Bianca, Snowy 1.3.1 Commercial
CASAVA CASAVA Rackham, Irma, Bianca, Snowy 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, 4.0.0, 5.0.1, 6.0.2, 6.1.2 other
Cell Ranger ARC (Chromium 10X) cellranger-ARC Rackham, Irma, Bianca, Snowy 1.0.0 other
Cell Ranger DNA (Chromium 10X) cellranger-DNA Rackham, Irma, Bianca, Snowy 1.1.0 other
EMBOSS emboss Rackham, Irma, Bianca, Snowy 6.6.0 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 Rackham, Irma, Bianca, Snowy 3.6, 3.7, 3.8-0 MIT + academic non-commercial
GenomeSTRiP GenomeSTRiP Rackham, Irma, Bianca, Snowy 2.00.1650, 2.00.1685, 2.00.1710 Custom 'as is' redistributable
HiSeq HiSeq Rackham, Irma, Bianca, Snowy 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 Rackham, Miarka, Bianca, Snowy 5.0.1, 5.5.1 BSD Style
SpeedSeq SpeedSeq Rackham, Irma, Bianca, Snowy 0.1.2-20170504-30f8dc6, 0.1.2-20180208-4e60002 MIT
Staden staden Rackham, Irma, Bianca, Snowy 2.0.0b6 BSD
Supernova (Chromium 10X) supernova Rackham, Irma, Bianca, Snowy 1.0.0, 1.1.1, 1.1.4, 2.0.0 other
vcfstats vcfstats Rackham, Irma, Bianca, Snowy 0.4.2,
VCFtools vcftools Rackham, Irma, Bianca, Snowy 0.1.12, 0.1.13, 0.1.14, 0.1.15, 0.1.16 GPL v3
Last modified: 2023-05-30