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+ |
| 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 | 2.26, 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, 2.24.0, 2.28.0 | 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, Irma, Bianca, Snowy | 1.1.1 | 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 |
| 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 | 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 | 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 | 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 |
| MOLDEN | molden | Rackham | 5.1 | |
| PRISMS-PS | PRISMS-PF | Rackham, Snowy | 2.1.1 | Lesser GPL |
| 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 | 1.9.5, 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, Irma, Bianca, Snowy | 3.5.0, 3.9.1-gcc9.3.0 | 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 | 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 | MIT |
| 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 | 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 |
| NONMEM | nonmem | Rackham, Irma, Bianca, Snowy | 7.4.3, 7.4.3-intel | commercial |
| Perl-speaks-NONMEM | PsN | Rackham, Irma, Bianca, Snowy | 5.0.0 | 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. 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, 4.0.0, 4.0.4 | GPL, LGPL. and others |
| RStudio | RStudio | Rackham, Irma, Bianca, Snowy | 1.0.136, 1.0.143, 1.0.153, 1.1.423, 1.1.463, 1.4.1106 | 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 |
| 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 | 3.5.1, 3.7.2, 3.13.2, 3.17.3 | 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 |
| 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 |
| 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 | 1.16.0.2, 2.2.3.2, 2.10.1 | GPL v2 |
| 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 |
| Texinfo | texinfo | Rackham, Irma, Bianca, Snowy | 6.0, 6.5, 6.6, 6.8 | GPL v3 |
| TeX Live | texlive | Rackham, Irma, Bianca, Snowy | 2015, 2016, 2018, 2019, 2021 | 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, Irma, Bianca, Snowy | 5.2.2 | Mixed |
| VIM | vim | Rackham, Irma, Bianca, Snowy | 7.4-1941, 8.0-16, 8.0-1360, 8.1-1053 | Custom |
| 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, Irma, Bianca, Snowy | 1.0.6 | 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, Irma, Bianca, Snowy | 1.16, 2.1, 2.3, 2.5, 2.6 | 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, Irma, Bianca, Snowy | 7.45.0 | Custom open source "as is" |
| libHaru | libharu | Rackham, Irma, Bianca, Snowy | 2.3.0 | ZLIB/LIBPNG License |
| 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" |
| scalapack | scalapack | Milou | 1.8.0 | |
| Sodium | libsodium | Rackham, Irma, Bianca, Snowy | 1.0.18-stable | ISC |
| slurm-drmaa | slurm-drmaa | Rackham, Irma, Bianca, Snowy | 1.1.2-slurm19.05.8 | GPL v3 |
| sparsehash | sparsehash | Milou, Rackham, Irma, Bianca | 2.0.2, 2.0.3 | |
| 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, Irma, Bianca, Snowy | 1.2.8, 1.2.11 | ZLIB License |
| 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 | Milou, Rackham, Irma, Bianca | 0.7.12 | GPL |
| 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 | 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 | 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, 2018-02-12, 2018-07-04, 2021-03-08 | 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 | Milou, Rackham, Irma, Bianca | 1.1.1, 1.1.2 | BSD |
| 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 | 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, 2.17-r941, 2.18-r1015 | 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, 4.0.0rc1 | Artistic License 2.0 |
| 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 | Rackham, Irma, Bianca, Snowy | 2.0, 2.1 | Same as blat |
| pblat-cluster | pblat-cluster | Rackham, Irma, Bianca, Snowy | 0.1, 0.3, 1.0 | Same as blat |
| pfam_scan | pfam_scan | Rackham, Irma, Bianca, Snowy | 1.3, 1.5, 1.6 | GPL v3 |
| pplacer | pplacer | Milou, Rackham, Irma, Bianca | 1.1.alpha19 | GPL v3 |
| PRANK | prank | Rackham, Irma, Bianca, Snowy | 150803, 170427 | 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 | Rackham, Irma, Bianca, Snowy | 2.1.4, 2.3.1, 2.4.0 | 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 | 1.3.1 | GPL |
| 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 | 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, 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, 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 |
| 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 | Artistic License 2.0 |
| 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 |
| 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 | 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 | 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 |
| 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" |
| 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 |
| 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 | MIT/Expat or GPL v3 |
| 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 |
| BioBakery (Metapackage that includes MetaPhlAn, PhyloPhlan, KneadData and HUMAnN) |
BioBakery | Rackham, Irma, Bianca, Snowy | 3.0 | MIT |
| 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 | 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 | 1.4.4-u7, 1.4.5, 1.4.5-4e44b43 | GPL 3 |
| 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 | 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 |
| 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, 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 | |
| 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 | 0.20.0 | 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 | GPL |
| 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 | 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, 1.3.2 | 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 | Rackham, Irma, Bianca, Snowy | 1.26.0, 1.93.2beta | 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, Irma, Bianca, Snowy | 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 | 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 |
| 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 | 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 | Rackham, Irma, Bianca, Snowy | 1.3, 1.3.2, 1.4, 1.5, 1.6, 1.8, 1.9, 1.10, 1.12 | MIT/Expat and modified 3-clause BSD |
| HTSeq | htseq | Rackham, Irma, Bianca, Snowy | 0.9.1, 0.12.4 | 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 | |
| KmerGenie | KmerGenie | Milou, Rackham, Irma, Bianca | 1.6741, 1.7039 | Other |
| KneadData | KneadData | Snowy, Rackham, Irma, Bianca | 0.10.0 | MIT |
| 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 |
| 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 |
| 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, 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 |
| mergeSVcallers | mergeSVcallers | Milou, Rackham, Irma, Bianca | 161006-23533ef | |
| MetaBAT | MetaBat | Milou, Rackham, Irma, Bianca | 0.26.3, 2.12.1 | BSD-like |
| 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 |
| 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 | 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 | 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 |
| NGSadmix | NGSadmix | Milou, Rackham, Irma, Bianca | 32 | |
| ngsplot | ngsplot | Milou, Rackham, Irma, Bianca | 2.61, 2.63 | GPL v2 |
| NgsRelate | NgsRelate | Snowy, Rackham, Irma, Bianca | 2.0 | 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 |
| NPStat | NPStat | Rackham, Irma, Bianca, Snowy | 1 | GPL version 3 |
| nseg | nseg | Rackham, Irma, Bianca, Snowy | 1.0.1 | Public Domain |
| 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 | Milou, Rackham, Irma, Bianca | 2.0.9 | |
| PCAngsd | PCAngsd | Rackham, Irma, Bianca, Snowy | 0.982 | 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 |
| 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, Irma, Bianca, Snowy | 2.00-alpha-2-20180704, 2.00-alpha-2-20190429, 2.00-alpha-2.3-20200124 | 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 | 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+ |
| 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 | 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 | 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 | GPL v3 |
| SMC++ | SMC++ | Rackham, Irma, Bianca, Snowy | 1.15.2 | 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 | Snowy, Rackham, Irma, Bianca | 4.0, 4.0.5, 4.6.0 | GPL 2.0 |
| 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 |
| 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 | 1.48, 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 |
| 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 | 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 | 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 |
| 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 |
| 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 |
| 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 | Milou, Rackham, Irma, Bianca | 4.6, 4.9e | Other |
| PathPhynder | pathPhynder | Rackham, Irma, Bianca, Snowy | 2020-12-19 | MIT |
| Phast | phast | Rackham, Irma, Bianca, Snowy | 1.4, 1.5 | 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, Irma, Bianca, Snowy | 2020-08-17 | 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 | 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 | 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 | |
| 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 | |
| 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 | 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, Irma, Bianca, Snowy | 5.0.1 | 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 |
| 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: 2021-10-25