Installed Software
Below you will find a list of software that's available on our resources via our module system. These are loaded with the "module load DESIRED_MODULE/VERSION" command. Depending on which cluster you're logged in to you will have access to different modules/software packages. List available modules with "module avail". More information about UPPMAX module system.
Notice: Before you can load any bioinformatics software, you will have to issue the command "module load bioinfo-tools".
If you are having trouble loading one of several build-related tools, including autoconf, automake, m4, sparsehash, and cmake, you may need to issue the command "module load build-tools".
UPPMAX buys, supports and updates software for scientific computing of general interest for researchers. The software is mainly made available on UPPMAX computer systems, but also on other computer systems within Uppsala University, when license agreements allows it. Examples of software are compilers (C, C++, F90) and software for electronic structure calculations, GAUSSIAN and GAMESS-US.
For information on how to use and write MPI and OpenMP parallel programs on Milou and Rackham, see the tutorial.
For support, please email support@uppmax.uu.se.
List of Software
| Software | Module | Cluster | Version | License |
|---|---|---|---|---|
| Compilers and build tools | ||||
| Allinea DDT | ddt | Milou, Rackham, Irma, Bianca | 3.2.1, 6.0 (Milou); 7.0 (Rackham, Irma, Bianca) | Commercial |
| Ant | ant | Milou, Rackham, Irma, Bianca | 1.8.1, 1.9.8, 1.10.0 | Apache 2.0 |
| autoconf | autoconf (load build-tools module for access) | Milou, Rackham, Irma, Bianca | 2.69 | GPL |
| automake | automake | Rackham, Irma, Bianca, Snowy | 1.14.1, 1.16.1 | GPL |
| Gnu binutils | binutils | Milou, Rackham, Irma, Bianca | 2.26 (Milou), 2.28 | GPL v2, v3; LGPL v2, v3 |
| gcc | gcc | Milou, Rackham, Irma, Bianca | 4.x, 5.x, 6.x | gpl |
| Git | git | Milou, Rackham, Irma, Bianca | 2.5.0, 2.10.2, 2.16.1 | LGPL 2.1 |
| Guile | guile | Milou, Rackham, Irma, Bianca | 1.8.8 | LGPL 2.1 |
| intel | intel | Milou, Irma, Rackham | site license, 2 users | |
| Java JDK | java | Milou, Rackham, Irma, Bianca | 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 | Milou | 0.3.0 pre-release | MIT |
| libtool | libtool | Milou, Rackham, Irma, Bianca | 2.4.6 | GPL |
| LLVM | llvm | Milou | ||
| m4 | m4( load build-tools module for access) | Milou, Rackham, Irma, Bianca | 1.4.17 | GPL |
| Maven | maven | Rackham, Irma, Bianca, Snowy | 3.6.0 | Apache 2.0 |
| Meson | meson | Rackham, Irma, Bianca, Snowy | 0.49.2 | Apache 2.0 |
| Mono | mono | Milou, Rackham, Irma, Bianca | 3.12.0 | Custom open source |
| Ninja | ninja | Rackham, Irma, Bianca, Snowy | 1.9.0 | Apache 2.0 |
| Open64 | open64 | Milou | ||
| patchelf | patchelf | Rackham, Irma, Bianca, Snowy | 0.8 | GPL v3 |
| Perl | perl | Rackham, Irma, Bianca, Snowy | 5.18.2, 5.18.4, 5.22.2, 5.24.0, 5.24.1, 5.26.2 (5.24+ build with 64-bit ints and pointers) | GPL, Perl |
| Perl Modules/Packages (large collection) | perl_modules | Milou, Rackham, Irma, Bianca | 5.18.4, 5.24.1 | GPL, Perl |
| Perl 6 | perl6 | Milou, Rackham, Irma, Bianca | rakudo-star-2017.04 | Artistic License 2.0 |
| pgi | pgi | Milou, Rackham | site license, 5 users | |
| Python | python | Rackham, Irma, Bianca, Snowy | 2.7.6, 2.7.9, 2.7.11, 2.7.15, 3.3, 3.3.1, 3.4.3, 3.5.0, 3.6.0, 3.6.8, 3.7.2 | GPL |
| Python 3 | python3 | Milou, Rackham, Irma, Bianca | 3.6.0 | GPL |
| Ruby | ruby | Milou, Rackham, Irma, Bianca | 2.0.0_p353 (Milou), 2.4.1, 2.5.0 | Ruby license |
| Subversion | subversion | Milou, Rackham, Irma, Bianca | 1.9.3 | Apache 2.0 |
| SunStudio | sunstudio | Milou | 12.1, 12.1u1 | |
| TotalView | totalview | Milou | 8.10.0-1, 8.8.0-2, 8.9.2-0, 8.9.2-2 | |
| Chemistry/Physics | ||||
| Gaussian |
g03 g09 |
Milou, Tintin | g03.d02, g03.e01, g09.a02, g09.c01, g09.d01 |
UU site license |
| turbomole | turbo | Rackham, Bianca, Irma, Snowy | 7.3 | proprietary group license |
| TmoleX | TmoleX | Rackham, Irma, Bianca, Snowy | 18 | proprietary group license |
| gamess | gamess | Milou | 20110811R1 20101001R1 20070324R1 | academic site license |
| VASP | vasp | Milou, Rackham | 4.6.34, 5.2.8, 5.2.11, 5.2.12, 5.4.1 | user group license |
| molcas | molcas | Milou | 7.8.082, 8.0.15-03-08 | user group license |
|
gromacs |
gromacs | Milou, Rackham | 4.5.5, 4.6.3, 4.6.5, 5.0.4, 5.1.1 | gpl |
|
desmond |
desmond | Milou | 2.2, 2.4, 2.4.2.1 | gpl |
| nonmem | nonmem | Milou | 7.1.0, 7.1.2, 7.2.0, 7.3.0 | |
| MOLDEN | molden | Rackham | 5.1 | |
| Engineering | ||||
| Matlab | matlab | Milou, Rackham | 7.4, 7.8, 7.10, 7.13, 8.0, 8.1, R2014a, R2015a, R2015b, R2016a | site license |
| envi | envi | Milou | 4.8 | |
| openfoam | openfoam | Rackham | 2.4.0, v1612+ | |
| Comsol | comsol | Rackham, Milou | 4.4, 5.2a | UU site license |
| Geospatial | ||||
| GDAL | GDAL | Milou, Rackham, Irma, Bianca | 2.1.0 | X/MIT style Open Source |
| GEOS | GEOS | Milou, Rackham, Irma, Bianca | 3.5.0 | LGPL |
| libgeotiff | libgeotiff | Milou, Rackham, Irma, Bianca | 1.4.1 | X-style and custom open-source "as is" |
| OpenFYBA / SOSI | FYBA | Milou, Rackham, Irma, Bianca | 4.1.1 | Custom open-source "as is" |
| PROJ.4 | PROJ.4 | Milou, Rackham, Irma, Bianca | 4.9.2 | MIT |
| Statistics | ||||
| JAGS | JAGS | Rackham, Irma, Bianca | 4.2.0, 4.3.0 | GPL v2 |
| R | R | Milou, Rackham, Irma, Bianca | 2.10.1, 2.11.1, 2.12.1, 2.12.2, 2.13.0, 2.14.0, 2.15.0, 2.15.1, 2.15.2, 2.8, 2.8.1, 3.0.1, 3.0.2, 3.2.2 (from here on, built with gcc/4.9.2 and java/sun_jdk1.8.0_40), 3.2.3, 3.3.0, 3.3.1, 3.3.2, 3.4.0, 3.4.3, 3.5.0 | GPL |
| R packages | R_packages | Milou, Rackham, Irma, Bianca | 3.3.0, 3.3.1, 3.3.2, 3.4.0, 3.4.3, 3.5.0 (exhaustive) | |
| RStudio | RStudio | Rackham, Irma, Bianca, Snowy | 1.0.136, 1.0.143, 1.0.153, 1.1.423, 1.1.463 | AGPL |
| stata | stata | Milou | 12 | |
| Misc Applications | ||||
| agrep | agrep | Milou, Rackham, Irma, Bianca | 3.41.5 | ISC Open Source |
| albacore | albacore | Rackham, Irma, Bianca, Snowy | build-4aee41d | GPL3 |
| Amazon Web Services Command Line Interface | awscli | Milou, Rackham, Irma, Bianca | 1.9.6, 1.11.140 | Apache 2.0 |
| blobtools | blobtools | Rackham, Irma, Bianca | 1.0 | |
| Circos | circos | Milou | 0.66 | |
| CMake | cmake | Rackham, Irma, Bianca, Snowy | 2.8.6, 2.8.11.2, 2.8.12.2, 3.5.1, 3.7.2, 3.13.2 | BSD 3-Clause |
| Cowsay | cowsay | Milou, Rackham, Irma, Bianca | 3.03 | Artistic License |
| Doxygen | doxygen | Milou, Rackham, Irma, Bianca | 1.8.9.1, 1.8.11 | Gnu GPL 2 |
| eLSA | eLSA | Milou, Rackham, Irma, Bianca | eLSA/20160907-febe2d7a57c8 | |
| GNU Emacs | emacs | Milou, Rackham, Irma, Bianca | 25.2 | GPL v3 |
| Gnu awk | gawk | Milou, Rackham, Irma, Bianca | 4.1.4 | GPL v3 |
| gnuplot | gnuplot | Milou, Rackham, Irma, Bianca | 4.4.3, 4.6.5, 5.0.7 | Custom open-source "as-is" |
| groff | groff | Milou, Rackham, Irma, Bianca | 1.22.3 | GPL |
| h5utils | h5utils | Milou, Rackham, Irma, Bianca | 1.12.1 | GPL v2+ |
| Haskell Tool Stack | haskell-stack | Milou, Rackham, Irma, Bianca | 1.0.4.3, 1.4.0 | Custom "as is" |
| ImageMagick | ImageMagick | Milou, Rackham, Irma, Bianca | 6.9.9-35 | Apache 2.0 |
| MariaDB | MariaDB | Milou, Rackham, Irma, Bianca | 10.1.29, 10.2.11 | GPL v2 |
| mbuffer | mbuffer | Milou, Rackham, Irma, Bianca | 20151002 | GPL v3 |
| MCL | mcl | Milou, Rackham, Irma, Bianca | 14-137 | GPL v3 |
| p7zip | p7zip | Milou, Rackham, Irma, Bianca | 16.02 | LGPLv2 |
| PostgreSQL | PostgreSQL | Milou, Rackham, Irma, Bianca | 10.3 | PostgreSQL Licence |
| POV-Ray | povray | Rackham, Irma, Bianca | 3.7 | AGPL v3 |
| ROOT | ROOT | Milou, Rackham, Irma, Bianca | 6.04.08, 6.06.08 | LGPL v2.1 |
| rvtests | rvtests | Rackham, Irma, Bianca | 2.0.6 | |
| SCons | SCons | Milou, Rackham, Irma, Bianca | 2.5.0 | misc free software |
| SWIG | swig | Milou, Rackham, Irma, Bianca | 3.0.7 | GPL v3 plus some "as is" |
| SQLite | sqlite | Milou, Rackham, Irma, Bianca | (system), 3.8.5, 3.11.1, 3.16.2 | Public domain |
| Texinfo | texinfo | Milou, Rackham, Irma, Bianca | 6.0 | GPL v3 |
| TeX Live | texlive | Milou, Rackham, Irma, Bianca | 2015, 2016 | misc free software |
| tinyutils | tinyutils | Milou, Rackham, Irma, Bianca | 1.1, 1.2, 1.3, 1.4 | GPLv2 |
| tmux | tmux | Milou | 1.9a | |
| XZ Utils | xz | Milou, Rackham, Irma, Bianca | 5.2.2 | Mixed |
| VIM | vim | Milou, Rackham, Irma, Bianca | 7.4-1941, 8.0-16, 8.0-1360 | Custom |
| Parallel | ||||
| mpjexpress | mpjexpress | Milou | 0.38 | |
| intelmpi | intelmpi | Milou, Irma, Rackham | 5.1.2, 5.1.3, 17.0, 17.1, 17.2 | |
| openmpi | openmpi | Milou, Irma, Rackham | 1.4, 1.4.4, 1.45, 1.5, 1.5.5, 1.6, 1.6.3, 1.6.4, 1.7, 1.7.0, 1.7.1, 1.10.0, 1.10.1, 1.10.2, 2.0.1, 2.0.2 | GPL |
| GNU parallel | gnuparallel | Rackham, Irma, Bianca, Snowy | 20170122, 20180822 | GPL |
| Libraries | ||||
| Armadillo | Armadillo | Milou, Rackham, Irma, Bianca | 20170510 | Apache License 2.0 |
| ATLAS | ATLAS | Milou, Rackham, Irma, Bianca | 3.10.3 | BSD-style |
| BLAS and CBLAS | blas | Milou, Rackham, Irma, Bianca | 3.6.0 | Open source |
| Boost | boost | Milou, Rackham, Irma, Bianca | 1.55.0, 1.59.0_gcc4.9.2, 1.59.0_intel15.3, 1.61.0_gcc5.3.0, 1.63.0_gcc6.3.0, 1.63.0_gcc6.3.0_mpi2.0.2 | Boost licence |
| bzip2 | bzip2 | Milou, Rackham, Irma, Bianca | 1.0.6 | Custom open source "as is" |
| Cairo | cairo | Milou, Rackham, Irma, Bianca | 1.14.8 | GNU LGPL v2.1 or Mozilla Public Licence 1.1 |
| fftw | fftw | Milou | 2.1.5, 3.2.2 | |
| FreeType | freetype | Milou, Rackham, Irma, Bianca | 2.6, 2.7.1 | BSD-like FreeType and GPL v2 |
| GIFLIB | giflib | Milou, Rackham, Irma, Bianca | 5.1.4 | Custom "as is" |
| GLPK | glpk | Rackham, Irma, Bianca | 4.63 | GPL |
| Gnu Scientific Library | gsl | Milou, Rackham, Irma, Bianca | 1.16, 2.1, 2.3 | GPL |
| HDF4 | hdf4 | Milou, Rackham, Irma, Bianca | 4.2.11_gcc4.9.2 | BSD-style open source |
| HDF5 | hdf5 | Milou, Rackham, Irma, Bianca | 1.8.16_gcc4.9.2, 1.8.18, 1.8.18_gcc6.3.0 | BSD-style open source |
| jemalloc | jemalloc | Milou, Rackham, Irma, Bianca | 3.6.0, 5.0.1 | BSD-derived |
| libcurl | libcurl | Milou, Rackham, Irma, Bianca | 7.45.0 | Custom open source "as is" |
| libHaru | libharu | Milou, Rackham, Irma, Bianca | 2.3.0 | ZLIB/LIBPNG License |
| NetCDF | netcdf | Milou (4.4.0) | 4.4.0 | Custom open source "as is" |
| OpenBLAS | openblas | Milou, Rackham, Irma, Bianca | 0.2.14a, 0.2.19 | BSD 3-clause |
| PCRE | pcre | Milou, Rackham, Irma, Bianca | 8.38, 8.40 | BSD 3-clause |
| Poppler | Poppler | Milou, Rackham, Irma, Bianca | 0.43.0, 0.54.0 | GPL v2 |
| scalapack | scalapack | Milou | 1.8.0 | |
| sparsehash | sparsehash | Milou, Rackham, Irma, Bianca | 2.0.2, 2.0.3 | |
| SZIP | szip | Milou, Rackham, Irma, Bianca | 2.1_gcc4.9.2, 2.1.1 | BSD-style open source |
| Intel Threading Building Blocks | tbb | Milou | 4.4u1_gcc4.9.2, 4.4u1_intel15.3 | GPL v2 |
| UDUNITS | UDUNITS | Rackham, Irma, Bianca | 2.2.26 | Custom open source "as is" |
| Yeppp | Yeppp | Milou, Rackham, Irma, Bianca | 1.0.0 | Custom open source "as is" |
| zlib | zlib | Milou, Rackham, Irma, Bianca | 1.2.8, 1.2.11 | ZLIB License |
| Bioinformatics Alignment | Module | Cluster | Version | License |
| AGE | AGE | Milou, Rackham, Irma, Bianca | 0.4 | |
| ANFO | anfo | Milou, Rackham, Irma, Bianca | 0.98 | GPL |
| ARAGORN | aragorn | Milou, Rackham, Irma, Bianca | 1.2.36, 1.2.38 | |
| Barrnap | barrnap | Milou, Rackham, Irma, Bianca | 0.2, 0.6, 0.8 | |
| Blasr and associated utilities | blasr | Rackham, Irma, Bianca, Snowy | 20150922, 5.3-20161121-e901e48, 5.3-20171117-f72428d, 5.3.2 | Open source redistributable "as is" |
| BLAST (legacy) | blast | Milou, Rackham, Irma, Bianca | 2.2.15, 2.2.18, 2.2.22, 2.2.23, 2.2.24, 2.2.25, 2.2.26 | Public Domain |
| BLAST | blast | Milou, Rackham, Irma, Bianca | 2.2.23+, 2.2.24+, 2.2.25+, 2.2.27+, 2.2.28+, 2.2.29+, 2.2.31+, 2.4.0+, 2.5.0+, 2.6.0+, 2.7.1+ | Public Domain |
| BLAT | blat | Milou, Rackham, Irma, Bianca | 34, 35 | Other |
| BWA | bwa | Milou, Rackham, Irma, Bianca | 0.5.8a, 0.5.9, 0.6.1, 0.6.2, 0.7.4, 0.7.5a, 0.7.8, 0.7.10, 0.7.12, 0.7.13, 0.7.15, 0.7.17 | GPL |
| bwa.kit | bwakit | Milou, Rackham, Irma, Bianca | 0.7.12 | GPL |
| ClustalO | clustalo | Milou, Rackham, Irma, Bianca | 1.2, 1.2.4 | |
| ClustalW | clustalw | Milou, Rackham, Irma, Bianca | 2.1 | LGPL |
| DIAMOND | diamond | Milou, Rackham, Irma, Bianca | 0.7.9, 0.7.12, 0.8.26, 0.9.10 | Other open-source |
| Exonerate | exonerate | Milou, Rackham, Irma, Bianca | 2.2.0 | |
| FASTA | fasta | Milou | 36.3.6d, 36.3.6f, 36.3.8 | Apache 2.0 |
| GeneID | geneid | Milou, Rackham, Irma, Bianca | 1.4.4 | GPL |
| GMAP-GSNAP | gmap-gsnap | Rackham, Irma, Bianca, Snowy | 2014-01-21, 2015-09-28, 2016-05-01, 2017-09-11, 2018-02-12, 2018-07-04 | Custom as-is |
| HAL | hal | Milou, Rackham | 20151218, 20161130 | open-source "as is" and others |
| HISAT2 | HISAT2 | Milou, Rackham, Irma, Bianca | 2.0.1-beta, 2.0.5, 2.1.0 | GPL |
| HMMER | hmmer | Milou, Rackham, Irma, Bianca | 2.3.2-gcc, 2.3.2-intel, 3.0, 3.1b1, 3.1b2, 3.1b2-intel (MPI support, compiled with intel/17.2 and openmpi/2.1.0) | GPL |
| Infernal | infernal | Milou, Rackham, Irma, Bianca | 1.1.1, 1.1.2 | BSD |
| LAST | last | Milou, Rackham, Irma, Bianca | 847 | GPL v3 |
| LASTZ | lastz | Milou, Rackham, Irma, Bianca | 1.03.54, 1.04.00 | |
| LEON-BIS | LEON-BIS | Milou, Rackham, Irma, Bianca | 20130322 | |
| MAFFT | MAFFT | Milou, Rackham, Irma, Bianca | 7.205, 7.245, 7.310, 7.407 | BSD (main), mixed open-source (extensions) |
| MafFilter | MafFilter | Milou, Rackham, Irma, Bianca | 1.1.2 | |
| mafTools | mafTools | Milou | 20141112 | "As is" open source |
| Maq | maq | Milou, Rackham, Irma, Bianca | 0.7.1 | GPL |
| MinCED | minced | Milou, Rackham, Irma, Bianca | 0.2.0 | GPL v3 |
| Minimap2 | minimap2 | Milou, Rackham, Irma, Bianca | 2.4 | MIT |
| MOSAIK | mosaik-aligner | Milou, Rackham, Irma, Bianca | 1.0.1388, 1.1.0021, 2.2.3, 2.2.26, 2.2.30 | GPL |
| MPIBlast | mpiblast | Milou | 1.6.0 | GPL |
| Multiz | multiz | Milou, Rackham, Irma, Bianca | 012109 | |
| MUMmer | MUMmer | Rackham, Irma, Bianca, Snowy | 3.22, 3.23, 3.9.4alpha, 4.0.0beta2 | Artistic License 2 |
| MUSCLE | muscle | Milou, Rackham, Irma, Bianca | 3.8.31, 3.8.1551 | Public domain |
| Nextflow | Nextflow | Milou, Rackham, Irma, Bianca | 0.17.3, 0.22.2, 0.26.0 | GPLv3 |
| NextGenMap | NextGenMap | Milou, Rackham, Irma, Bianca | 0.4.12, 0.5.4 | Artistic License 1.0 |
| OMBlast | OMBlast | Milou, Rackham, Irma, Bianca | 1.0 | unknown |
| OPTIMA | optima | Milou, Rackham, Irma, Bianca | f-1.3 | GPL v2 |
| pblat | pblat | Milou, Rackham, Irma, Bianca | 1.6, 2.0 | Same as blat |
| pblat-cluster | pblat-cluster | Milou, Rackham, Irma, Bianca | 0.1, 0.3 | Same as blat |
| pfam_scan | pfam_scan | Milou, Rackham, Irma, Bianca | 1.3, 1.5, 1.6 | GPL v3 |
| pplacer | pplacer | Milou, Rackham, Irma, Bianca | 1.1.alpha19 | GPL v3 |
| PRANK | prank | Milou, Rackham, Irma, Bianca | 150803, 170427 (not milou) | GPL v2+ |
| ProbCons | ProbCons | Milou, Rackham, Irma, Bianca | 1.12 | Public domain |
| progressiveCactus | progressiveCactus | Milou | 2015-02-06, 2015-12-18, 2016-11-30 | GPL v3, mostly |
| QualiMap | QualiMap | Milou, Rackham, Irma, Bianca | 2.0.2, 2.2 | GPL |
| RNAmmer | rnammer | Milou, Rackham, Irma, Bianca | 1.2 | |
| SiBELia | SiBELia | Milou, Rackham, Irma, Bianca | 3.0.6 | |
| SortMeRNA | SortMeRNA | Milou, Rackham, Irma, Bianca | 2.1b | GPL v3 |
| Spaln | spaln | Milou, Rackham, Irma, Bianca | 2.3.1 | GPL v2 |
| SplitSeek | splitseek | Milou | 1.3.2, 1.3.3, 1.3.4 | GPL |
| Stampy | Stampy | Rackham, Irma, Bianca, Snowy | 1.0.27, 1.0.32 | Custom (non-commercial) |
| T-Coffee | T-Coffee | Milou, Rackham, Irma, Bianca | 11.00.8cbe486 | GPL v2 |
| TRF | trf | Milou | 4.07b | |
| tRNAscan-SE | tRNAscan-SE | Milou, Rackham, Irma, Bianca | 1.3.1 | GPL |
| Vmatch | Vmatch | Milou, Rackham, Irma, Bianca | 2.2.5, 2.3.0 | Custom non-commercial |
| Vsearch | vsearch | Milou, Rackham, Irma, Bianca | 2.3.2, 2.4.3, 2.5.2 | Dual GPL/BSD |
| Wise2 | wise2 | Milou, Rackham, Irma, Bianca | 2.2.0, 2.4.1 | Other |
| Bioinformatics Annotation | Module | Cluster | Version | License |
| AAT | AAT | Milou, Rackham, Irma, Bianca | r03052011 | |
| Augustus | augustus | Milou, Rackham, Irma, Bianca | 2.7, 3.0.1, 3.2.1, 3.2.2, 3.2.3 | Artistic License |
| CEGMA | cegma | Milou, Rackham, Irma, Bianca | 2.4.010312, 2.5 | |
| Delly | delly | Milou, Rackham, Irma, Bianca | 0.0.11, 0.3.3, 0.6.3, 0.7.2, 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 | Milou, Rackham, Irma, Bianca | 0.16.3, 0.18.3, 0.19.0, 0.20.0 | MIT |
| GenomeThreader | GenomeThreader | Rackham, Irma, Bianca | 1.7.0 | Custom "AS IS" |
| HaMStR | HaMStR | Milou | 13.2.3 | GNU GPL 3 |
| InterProScan | InterProScan | Rackham, Irma, Bianca | 5.30-69.0 | Misc |
| MAKER | maker | Milou, Rackham, Irma, Bianca | 2.28, 2.31, 2.31.6, 2.31.8, 2.31.9, 3.01.1-beta | GPL |
| Phobius | Phobius | Rackham, Irma, Bianca | 1.01 | Private study, education and non-profit research only |
| Scipio | Scipio | Milou, Rackham, Irma, Bianca | 1.4.1 | Custom non-commercial |
| SignalP | SignalP | Milou, Rackham, Irma, Bianca | 4.1c, 4.1f | Custom academic user licence |
| sissrs | sissrs | Milou, Rackham, Irma, Bianca | 1.4 | Open source |
| snpEff | snpEff | Milou, Rackham, Irma, Bianca | 2.0.3, 2.0.5, 3.4, 3.6, 4.0, 4.1, 4.2, 4.3t | LGPL |
| TMHMM | tmhmm | Milou, Rackham, Irma, Bianca | 2.0c | Custom academic as-is |
| TransDecoder | TransDecoder | Milou, Rackham, Irma, Bianca | 2.0.1, 5.0.1 | Broad Institute redistributable as-is |
| Trinotate | trinotate | Milou, Rackham, Irma, Bianca | 2.0.1, 3.0.2 | |
| Bioinformatics Assembly | Module | Cluster | Version | License |
| A5-MiSeq | A5-miseq | Milou, Rackham | 20140113, 20140604, 20160825 | GPL |
| ABySS | abyss | Milou, Rackham, Irma, Bianca | 1.2.3, 1.2.4, 1.2.5, 1.2.7 1.2.7-maxk96, 1.3.0, 1.3.2, 1.3.3, 1.3.3-k96, 1.3.4, 1.3.5, 1.3.5-max, 1.3.7, 1.3.7-max, 1.3.7-k128, 1.5.2, 1.9.0, 1.9.0-k128, 2.0.2, 2.0.2-k128 | GPL v3 |
| AllPathsLG | allpathslg | Milou, Irma | 47300, 49618, 52485 | |
| AMOS | AMOS | Milou, Rackham, Irma, Bianca | 3.0.0, 3.1.0 | Artistic |
| ARC assembler | ARC_assembler | Milou | 1.1.3 | Apache 2.0 |
| BESST | BESST | Milou | 1.0.4.3, 1.0.4.4 | |
| CABOG (WGA assembler, Celera Assembler), includes PBcR | cabog, CA (synonym) | Milou, Rackham, Irma, Bianca | 8.1, 8.3 | GPL v2 and others for subcomponents |
| Canu | canu | Milou, Rackham, Irma, Bianca | 1.0, 1.1, 1.3, 1.5, 1.6, 1.7 | GPL v2 and others for subcomponents |
| DBG2OLC | DBG2OLC | Milou | 20151208 | |
| DISCOVAR de novo | DISCOVARdenovo | Milou | 51885 | Custom "as is" |
| FALCON | FALCON | Milou | 0.3.0, 0.4.1 | Custom "as is" |
| FALCON-integrate | FALCON-integrate | Milou | 20161113 | Custom "as is" |
| fermi | fermi | Milou, Rackham, Irma, Bianca | 1.1-r751-beta | |
| GAEMR | gaemr | Milou, Rackham, Irma, Bianca | 1.0.1 | |
| GARM | GARM | Rackham, Irma, Bianca | 0.7.3 | |
| IDBA | IDBA | Milou | 1.1.1 (max read length 128 bp), 1.1.1-384 (max 384 bp) | GPL 2 |
| Kourami | kourami | Rackham, Irma, Bianca, Snowy | 0.9.6 | BSD 3 |
| LoRDEC | LoRDEC | Rackham, Irma, Bianca, Snowy | 0.9 | CeCILL 2.1 |
| MaSuRCA | MaSuRCA | Milou, Rackham, Irma, Bianca | 2.0.3.1, 2.1.0, 2.3.2, 3.1.3, 3.2.1, 3.2.2, 3.2.3 | |
| MEGAHIT | megahit | Milou, Rackham, Irma, Bianca | 1.0.3, 1.1.2 | GPL v3 |
| MetAMOS | MetAMOS | Milou | 1.5rc3 | GPLv2 and other open source |
| Metassembler | Metassembler | Milou | 1.5 | open-source |
| MHAP | MHAP | Milou | 1.6 | Apache 2.0 |
| Miniasm | miniasm | Milou | 20160128 | MIT |
| Minimap | minimap | Milou, Rackham, Irma, Bianca | 20160114 | MIT |
| MIRA | mira | Milou | 3.0.0, 3.2.0, 3.4.0.1, 4.0.0rc4, 4.0.2 | GPL |
| Oases | oases | Milou | 0.2.08 | GPL |
| PBSuite (contains PBJelly and PBHoney) | PBSuite | Milou, Rackham, Irma, Bianca | 15.8.24 | Custom redistributable "as is" |
| Pilon | Pilon | Milou, Rackham, Irma, Bianca | 1.17, 1.22 | GPL v2 |
| Platanus | Platanus | Milou | 1.2.1 | |
| RACA (Reference-Assisted Chromosome Assembly) | RACA | Milou | 0.9.1.1 | |
| Ragout | Ragout | Milou, Rackham, Irma, Bianca | 2.0-20170312 | GPL v3.0 |
| Ray | Ray | Milou, Rackham, Irma, Bianca | 0.0.4, 0.0.7, 1.6.1, 2.3.0, 2.3.1, 2.3.1-mpiio (with support for MPI I/O, but this seems not to work very well) | GPL |
| REAPR | REAPR | Milou, Rackham, Irma, Bianca | 1.0.17, 1.0.18 | GPL |
| Redundans | Redundans | Milou, Rackham, Irma, Bianca | 0.13a-20170321 | GPL v2 |
| satsuma2 | satsuma2 | Milou, Rackham, Irma, Bianca | 2016-12-07 | LGPL v3+ |
| SGA | SGA | Milou, Rackham, Irma, Bianca | 0.10.14 | GPL v3 |
| SOAPcorrector | soapcorrector | Milou, Rackham, Irma, Bianca | 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 | Milou, Rackham, Irma, Bianca | 2.5.1, 3.0.0, 3.1.1, 3.5.0, 3.6.0, 3.6.1, 3.7.0, 3.7.1, 3.8.0, 3.8.1, 3.9.0, 3.10.0, 3.10.1, 3.11.1 | GPL v3 |
| StringTie | StringTie | Milou, Rackham, Irma | 1.2.0, 1.3.3 | Artistic |
| Tigmint | tigmint | Rackham, Irma, Bianca, Snowy | 1.1.2 | GPL v3 |
| Trans-ABySS | transabyss | Milou | 1.5.3 | BCCA "As Is" |
| Trinity | trinity | Milou, Rackham, Irma, Bianca | 2011-05-13, 2011-10-29, 2011-11-26, 2012-04-27, 2012-06-08, 2013-08-26, 2014-04-13, 2014-07-17, 2.0.2, 2.0.6, 2.1.0, 2.3.2, 2.4.0 | Other |
| Velvet | velvet | Milou, Rackham, Irma, Bianca | 1.0.03, 1.1.04, 1.1.04_K101, 1.1.07, 1.2.10, 1.2.10_K128 | GPL |
| Bioinformatics Misc | Module | Cluster | Version | License |
| AdapterRemoval | AdapterRemoval | Milou, Rackham, Irma, Bianca | 2.1.7, 2.2.2 | GPL v3 |
| AdmixTools | AdmixTools | Milou, Rackham, Irma, Bianca | 20160803, 5.0-20170312, 5.0-20171024 | Custom "as-is" open source |
| ADMIXTURE | ADMIXTURE | Milou, Rackham, Irma, Bianca | 1.3.0 | Not open source |
| ALDER | alder | Milou, Rackham, Irma, Bianca | 1.03 | Other |
| AlienTrimmer | AlienTrimmer | Milou, Rackham, Irma, Bianca | 0.4.0 | GPL |
| alleleCount | alleleCount | Milou, Rackham, Irma, Bianca | 2.2.0, 3.2.2 | GPL |
| ANGSD | ANGSD | Milou, Rackham, Irma, Bianca | 0.700, 0.902, 0.917, 0.917-g6522d3e, 0.921 | Open source |
| ANTs | ANTs | Rackham, Irma, Bianca, Snowy | 2.3.1 | Custom open-source "as is" |
| Artemis | artemis | Milou, Rackham, Irma, Bianca | 15.0.0, 16.0.0 | GPL |
| Athlates | Athlates | Milou, Rackham, Irma, Bianca | 20140426 | Custom |
| ATLAS | ATLAS_aDNA | Milou, Rackham, Irma, Bianca | 20170510 | |
| ATSAS | ATSAS | Milou, Rackham, Irma, Bianca | 2.8.3-1 | Academic use only |
| Bamtools | bamtools | Milou, Rackham, Irma, Bianca | 2.3.0, 2.5.1 | MIT |
| BCFtools | bcftools | Milou, Rackham, Irma, Bianca | 1.1, 1.2, 1.3, 1.3.1, 1.5 | MIT |
| BclConverter | Bclconverter | Milou, Rackham, Irma, Bianca | 1.7.1 | |
| bgc | bgc | Milou, Rackham, Irma, Bianca | 1.03 | GPL 3 |
| Beagle | beagle-app | Milou, Rackham, Irma, Bianca | 3, 4 | |
| BEETL | BEETL | Milou, Rackham, Irma, Bianca | 1.0.2, 1.1.0 | BSD 2-Clause |
| BioPerl | BioPerl | Milou, Rackham, Irma, Bianca | 1.6.1, 1.6.922, 1.6.923_Perl5.18.4, 1.6.924_Perl5.18.4 | Perl |
| BioPython | biopython | Rackham, Irma, Bianca, Snowy | 1.64 (loads python 2.7.6), 1.64-py3 (loads python 3.3.1), 1.65 (loads python 2.7.9), 1.65-py3 (loads python/3.4.3); 1.68 (loads python 2.7.6), 1.68-py3 (loads python/3.4.3); 1.73 (python/2.7.15), 1.73-py3 (python/3.6.0) | Biopython |
| Bismark | bismark | Milou, Rackham, Irma, Bianca | 0.12.2, 0.12.5, 0.13.0, 0.14.0, 0.14.5, 0.15.0, 0.16.1, 0.16.2, 0.16.3, 0.18.2 | GPL |
| BreakDancer | breakdancer | Milou, Rackham, Irma, Bianca | 1.4.4-u7, 1.4.5, 1.4.5-4e44b43 | GPL 3 |
| BRAKER | braker | Rackham, Irma, Bianca, milou | 2.1.1_Perl5.24.1 | Artistic License |
| BUSCO (with all lineage sets) | BUSCO | Milou, Rackham, Irma, Bianca | 1.1b1, 1.2, 1.22, 2.0.1, 3.0.2b | GPL v3+ |
| CD-Hit aka cdhit | cd-hit | Milou, Rackham, Irma, Bianca | 4.6.1, 4.6.4, 4.6.8-2017-1208 | GPL v2 |
| Cell Profiler | cellprofiler | Milou | 2.1.0 | |
| Centrifuge | Centrifuge | Rackham, Irma, Bianca | 1.0.4-beta | GPL v3 |
| CGAT | CGAT | Milou, Rackham, Irma, Bianca | 0.3.3 | "As is" |
| CheckM | CheckM | Rackham, Irma, Bianca, Snowy | 1.0.11, 1.0.12 | GPL v3 |
| CIRCexplorer | CIRCexplorer | Rackham, Irma, Bianca | 1.1.10 | |
| CleaveLand4 | CleaveLand4 | Milou, Rackham, Irma, Bianca | 4.3 | GPL v3 |
| cnD | cnD | Milou | 1.3 | GPL 3 |
| CNV-seq | CNV-seq | Milou | 20140812 | Misc open source |
| CNVnator | CNVnator | Milou, Rackham, Irma, Bianca | 0.3, 0.3.2, 0.3.3 | Creative Commons Public License |
| CONCOCT | CONCOCT | Rackham, Irma, Bianca, Snowy | 0.5.0 | FreeBSD |
| Corset | Corset | Milou, Rackham, Irma, Bianca | 1.04, 1.07 | GPL v3 |
| CRAM Tools | cramtools | Milou, Rackham, Irma, Bianca | 2.0, 3.0 | |
| deepTools | deepTools | Rackham, Irma, Bianca | 1.5.11 (milou only), 2.0.1, 2.2.3, 2.3.1, 2.4.3, 2.5.1, 3.1.0 | GPL v3 |
| DWGSIM | DWGSIM | Milou, Rackham, Irma, Bianca | 0.1.11-6e9a361 | GPL v2 |
| EEMS | eems | Milou, Rackham, Irma, Bianca | 20160605 | Misc open source |
| EIGENSOFT | eigensoft | Milou, Rackham, Irma, Bianca | 4.2, 5.0.1, 6.0.1 (long ID support), 6.1.2 (default ID). All following have long ID support. 6.1.4, 7.2.0, 7.2.1 | Custom |
| EMIRGE | emirge | Milou, Rackham, Irma, Bianca | 0.60 | GPL |
| EMMAX | emmax | Milou, Rackham, Irma, Bianca | Beta-07Mar2010 | GPL |
| EnsEMBL Perl API | EnsEMBL-API | Milou | 87 | Modified Apache |
| EPACTS | EPACTS | Milou, Rackham, Irma, Bianca | 3.2.6, 3.3.0-a5209db | GPL v3 |
| ExpansionHunter | ExpansionHunter | Milou, Rackham, Irma, Bianca | 2.5.3 | GPL v3 |
| eXpress | eXpress | Milou, Rackham, Irma, Bianca | 1.5.1 | Artistic License 2.0 |
| fastNGSadmix | fastNGSadmix | Milou, Rackham, Irma, Bianca | 20170825-099ab7f | |
| fastPHASE | fastPHASE | Milou, Rackham, Irma, Bianca | 1.4.0, 1.4.8 | Executable only |
| FastQC | FastQC | Milou, Rackham, Irma, Bianca | 0.6.1, 0.7.2, 0.10.1, 0.11.1, 0.11.2, 0.11.5 | GPL |
| fastq_screen | fastq_screen | Milou, Rackham, Irma, Bianca | 0.3.1, 0.4.3. 0.5.1, 0.9.2, 0.11.1 | GPL |
| FASTX | Fastx | Milou, Rackham, Irma, Bianca | 0.0.13, 0.0.13.2, 0.0.14 | AGPLv3 |
| fineSTRUCTURE | fineSTRUCTURE | Rackham, Irma, Bianca, Snowy | 4.0.1 | Free for noncommercial use only |
| FLASH | FLASH | Milou, Rackham, Irma, Bianca | 1.2.11 | GPL |
| flashpca | flashpca | Milou | 1.1.2.1 | GPL |
| fqzcomp | fqzcomp | Milou, Rackham, Irma, Bianca | 4.6 | |
| FreeBayes | freebayes | Milou, Rackham, Irma, Bianca | 0.8.9, 0.9.4, 0.9.4_2012-04-16, 0.9.8, 0.9.21, 1.0.2, 1.1.0 | Custom open-source "as-is" |
| FusionCatcher | FusionCatcher | Milou | 0.99.3e, 0.99.5a | GPL |
| GAM-NGS | gam-ngs | Milou | 1.1b | GPL |
| GCTA | gcta | Milou, Rackham, Irma, Bianca | 0.92.0, 0.92.6, 0.93.9, 1.26.0 | Public domain |
| GEM | GEM | Milou | 2.7 | "Research only" |
| GeneMark | GeneMark | Milou, Rackham, Irma, Bianca | 2.3-es (Milou), 4.32-es, 4.33-es | Other |
| GenomeTools | GenomeTools | Milou | 1.3.5 (Milou), 1.5.8 | BSD style |
| GERP++ | GERP++ | Milou | 20110522 | GPL v3+ |
| GTOOL | GTOOL | Milou | 0.7.5 | "As is" open source |
| gvcftools | gvcftools | Milou, Rackham, Irma, Bianca | 0.16.2, 0.17.0 | Various "As Is" open source |
| HiCExplorer | HiCExplorer | Milou, Rackham, Irma, Bianca | 2.2-beta | GPL v3 |
| HTSlib | htslib | Milou, Rackham, Irma, Bianca |
1.2.1, 1.3, 1.3.2, 1.4, 1.5, 1.6, |
MIT |
| HTSeq | htseq | Milou, Rackham, Irma, Bianca | 0.4.6, 0.5.1. 0.6.1, 0.9.1 | GPL |
| Integrative Genomics Viewer | IGV | Milou, Rackham, Irma, Bianca | 1.5.51, 2.3.17, 2.3.40, 2.3.92, 2.4.2 | LGPL |
| Integrative Genomics Viewer Tools | IGVtools | Milou, Rackham, Irma, Bianca | 2.2.1, 2.3.17, 2.3.40, 2.3.91, 2.3.98 | LGPL |
| IM | IM | Milou | 20091217 | |
| IMa2p | IMa2p | Milou | 2015-08-09 | GPL v3 |
| IMPUTE2 | IMPUTE2 | Milou, Rackham, Irma, Bianca | 2.3.2 | "As is" open source |
| ITSx | ITSx | Milou, Rackham, Irma, Bianca | 1.0.9, 1.0.11, 1.1-beta | GPL |
| Jellyfish | jellyfish | Milou, Rackham, Irma, Bianca | 1.1.11, 2.0.0, 2.1.4, 2.2.3-dev, 2.2.4, 2.2.6 | GPL |
| kallisto | kallisto | Milou, Rackham, Irma, Bianca | 0.42.4, 0.43.0, 0.43.1 | BSD 2-clause |
| KAT | KAT | Milou, Rackham, Irma, Bianca | 2.0.4, 2.0.6, 2.0.8, 2.1.1, 2.3.4, 2.4.2 | GPL v3 |
| Khmer | khmer | Milou, Rackham, Irma, Bianca | 1.4, 2.0, 2.1.1 | |
| KmerGenie | KmerGenie | Milou, Rackham, Irma, Bianca | 1.6741, 1.7039 | Other |
| Kraken | Kraken | Milou, Rackham, Irma, Bianca | 0.10.5-beta, 1.0, 1.1-352e780 | GPL v3 |
| Kraken2 | Kraken2 | Rackham, Irma, Bianca, Snowy | 2.0.7-beta-bc14b13 | 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 | Milou, Rackham, Irma, Bianca | 1.7, 1.9, 1.10 | GPL v3 |
| liftOver | liftOver | Milou, Rackham, Irma, Bianca | 2017-03-14 | |
| LTR Finder | ltr-finder | Milou | 1.0.5 | |
| LUMPY | LUMPY | Milou, Rackham, Irma, Bianca | 0.2.12, 0.2.13-213a417 | MIT |
| MACS | MACS |
Milou; Rackham, Irma, Bianca |
1.4.1, 1.4.2, 2.1.0; 2.1.2 |
Other |
| MACE | MACE | Milou | 1.2 | |
| MAGeCK | MAGeCK | Milou, Rackham, Irma, Bianca | 0.5.6 | BSD 3-clause |
| MALDER | malder | Rackham, Irma, Bianca | 1.0 | |
| manta | manta | Milou | 0.27.1, 1.0.0, 1.0.3 | GPL v3 |
| mapDamage | mapDamage | Milou, Rackham, Irma, Bianca | 2015-04-10 | Public Domain |
| matrix2png | matrix2png | Milou | 1.2.1 | Apache |
| MaxBin | MaxBin | Rackham, Bianca, Irma, Snowy | 2.2.5 | BSD |
| Meerkat | Meerkat | Milou | 0.189 | Misc non-commercial open source |
| MELT | MELT | Milou, Rackham, Irma, Bianca | 2.0.2 | Misc non-commercial |
| mergeSVcallers | mergeSVcallers | Milou, Rackham, Irma, Bianca | 161006-23533ef | |
| MetaBAT | MetaBat | Milou, Rackham, Irma, Bianca | 0.26.3, 2.12.1 | BSD-like |
| MetaSV | MetaSV | Milou, Rackham, Irma, Bianca | 0.5.4 | BSD 2-clause |
| Metaxa2 | Metaxa2 | Milou | 2.1.3 | GPL v3 |
| MethPipe | MethPipe | Milou, Rackham, Irma, Bianca | 3.4.3 | GPL v3+ |
| MethylDackel | MethylDackel | Milou, Rackham, Irma, Bianca | 0.2.1 | |
| MHC-PRG | MHC-PRG | Rackham, Irma, Bianca, Snowy | 1.00 | GPL v3 |
| micca | micca | Milou | 1.4.0 | GPL v3 |
| Mimar | mimar | Milou | 20101217 | |
| Minimac4 | Minimac4 | Rackham, Irma, Bianca, Snowy | 1.0.0 | GPL v3 |
| miRDeep2 | mirdeep2 | Milou, Rackham, Irma, Bianca | 2.0.0.5, 2.0.0.8 | |
| MMSEQ | mmseq | Milou | 1.0.8a | GPL |
| Mothur | Mothur | Rackham, Irma, Bianca, Snowy | 1.40.5, 1.41.0 | GPL v3 |
| MSMC | msmc | Milou, Rackham, Irma, Bianca | 2014-09-29, 0.1.0 | GPL |
| MultiQC | MultiQC | Rackham, Irma, Bianca, Snowy | 0.3.1, 0.3.1-py3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.2, 1.3, 1.5, 1.6, 1.7 | MIT |
| MuSIC2 | music2 | Rackham,Irma,Bianca, Snowy | 0.2 | MIT |
| MuTect | mutect | Milou, Rackham, Irma, Bianca | 1.1.5 | Other |
| NGSadmix | NGSadmix | Milou, Rackham, Irma, Bianca | 32 | |
| ngsplot | ngsplot | Milou, Rackham, Irma, Bianca | 2.61 | GPL v2 |
| NGSrich | ngsrich | Milou, Rackham, Irma, Bianca | 0.7.8 | |
| NGSUtils | NGSUtils | Milou, Rackham, irma, Bianca | 0.5.9 | Custom open source "as is" |
| nibabel | nibabel | Rackham, Irma, Bianca, Snowy | 2.3.3 | MIT + BSD |
| OpenMS | OpenMS | Milou | 2.0.0 | BSD + other |
| OptiType | OptiType | Milou, Rackham, Irma, Bianca | 1.3.1 | BSD 3-Clause |
| OrthoMCL | OrthoMCL | Milou, Rackham, Irma, Bianca | 2.0.9 | |
| PEAR | pear | Milou, Rackham, Irma, Bianca | 0.9.5, 0.9.10 | CC |
| PennCNV | PennCNV | Milou | 20151014 | Public domain |
| Pftools | pftools | Milou | 2.3 | |
| phantompeakqualtools | phantompeakqualtools | Milou, Rackham, Irma, Bianca | 1.1 | MIT |
| PhyloPhlAn | phylophlan | Milou, Rackham, Irma, Bianca | 0.99 | Custom "as is" open source |
| Picard | picard | Milou, Rackham, Irma, Bianca | 1.40, 1.41, 1.59, 1.64, 1.69, 1.85, 1.92, 1.114, 1.118, 1.119, 1.127, 1.141, 2.0.1, 2.10.3 | MIT |
| PileOMeth (continued by MethylDackel) | PileOMeth | Milou | 0.1.13 | |
| Pindel | pindel | Milou | 0.2.4w | GPL 3 |
| PLINK | plink | Milou, Rackham, Irma, Bianca | 1.07, 1.90b3n (formerly version 1.90), 1.90b4.9, 2.00-c1defe4 | GPL v3 |
| PLINK/SEQ | plinkseq | Milou, Rackham, Irma, Bianca | 0.08 (formerly mislabelled as 0.8), 0.10 | Other |
| 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 |
| Prodigal | prodigal | Milou, Rackham, Irma, Bianca | 2.60, 2.6.3 | GPL v3 |
| ProtExcluder | ProtExcluder | Milou, Rackham, Irma, Bianca | 1.1 | |
| PSORTb | psortb | Milou | 3.0 | GPL |
| pyGenomeTracks | pyGenomeTracks | Rackham, Irma, Bianca, Snowy | 2.1 | GPL v3 |
| PySam | pysam | Milou, Rackham, Irma, Bianca | 0.6, 0.7.7 (Python2 & 3), 0.8.3 (python 2.7.6), 0.8.3-py27 (python 2.7), 0.8.3-py3 (python 3.4.3), 0.9.1.4, 0.10.0, 0.13-python2.7.11, 0.13-python3.6.0 | MIT |
| qctool | qctool | Rackham, Irma, Bianca, Snowy | 1.4, 2.0.1 | "As is" open source |
| QuantiSNP | QuantiSNP | Milou | 2.2 | |
| QUAST | quast | Milou, Rackham, Irma, Bianca | 2.2, 2.3, 3.2, 4.5.4 | |
| QuorUM | QuorUM | Milou | 1.0.0 | GPL v3 |
| RDP Classifier | rdp-classifier | Milou, Rackham, Irma, Bianca | 2.2, 2.4 | |
| RDXplorer | RDXplorer | Milou | 3.2 | open source |
| RepeatMasker | RepeatMasker | Rackham, Irma, Bianca, Snowy | 4.0.7, 4.0.7_Perl5.24.1, 4.0.8 | open source |
| RepeatModeler | RepeatModeler | Rackham, Irma, Bianca, Snowy | 1.0.8_RM4.0.7, 1.0.11 | open source |
| RGT | RGT | Rackham, Irma, Bianca, Snowy | 0.11.6 | GPL v3+ |
| Roary | Roary | Milou | 3.4.3, 3.5.5, 3.6.2 | GPL v3 |
| RSEM | rsem | Milou | 1.2.12, 1.2.29 | GPL |
| RSeqC | rseqc | Milou, Rackham, Irma, Bianca | 2.3, 2.3.6, 2.3.9, 2.4, 2.6.1, 2.6.4 | |
| RTG Core non-commercial (aka rtg-core) | rtgcore | Milou, Rackham, Irma, Bianca | 3.8.3 | Custom non-commercial use only |
| RTG Tools (aka rtg-tools) | rtgtools | Milou, Rackham, Irma, Bianca | 3.7.1, 3.8.1, 3.8.3 | BSD |
| Sailfish | Sailfish | Milou | 0.8.0 | GPL v3+ |
| Salmon | Salmon | Milou, Rackham, Irma, Bianca | 0.6.0, 0.8.2, 0.9.1 | GPL v3+ |
| sambamba | sambamba | Milou, Rackham, Irma, Bianca | 0.5.9, 0.6.6 | GPL v2+ |
| samblaster | samblaster | Milou, Rackham, Irma, Bianca | 0.1.22, 0.1.24 | MIT |
| samplefq | samplefq | Milou, Rackham, Irma, Bianca | 0.2 | GPL v3 |
| samstat | samstat | Rackham, Irma, Bianca | 1.5.1 | GPL v3 |
| SAMtools | samtools | Milou, Rackham, Irma, Bianca | 0.1.7a, 0.1.8, 0.1.9, 0.1.12, 0.1.16, 0.1.18, 0.1.19, 1.1, 1.2, 1.3, 1.4, 1.5 | MIT |
| SBT (bloomtree) | SBT | Milou, Rackham, Irma, Bianca | 0.1, 0.3 | |
| Scalpel | scalpel | Milou, Rackham, Irma, Bianca | 0.5.2, 0.5.3 | MIT |
| Schmutzi | schmutzi | Milou | 20160424 | |
| SCORE-Seq | SCORE-Seq | Milou | 5.3 | |
| Selscan | selscan | Milou, Rackham, Irma, Bianca | 1.1.0 | GPL v3 |
| SeqAn | SeqAn | Milou, Rackham, Irma, Bianca | 1.4.2 | Other open-source |
| seqMINER | seqMINER | Milou | 1.3.3e | |
| seqtk | seqtk | Milou, Rackham, Irma, Bianca | 1.0-r31, 1.0-r57, 1.0-r68e, 1.2-r101 | MIT |
| SeqMonk | seqmonk | Milou, Rackham, Irma, Bianca | 0.21.0, 0.27.0, 0.32.1, 0.34.1, 1.36.0, 1.37.1 | GPL |
| SeqPrep | SeqPrep | Milou, Rackham, Irma, Bianca | 1.1 (formerly 2013-11-14), 1.2 | MIT |
| SeqTools | SeqTools | Milou, Rackham, Irma, Bianca | 4.20, 4.44.1 | Apache 2.0 |
| SHAPEIT | SHAPEIT | Milou, Rackham, Irma, Bianca | v2.r837 | Custom non-commercial |
| ShoRAH | ShoRAH | Milou, Rackham, Irma, Bianca | 1.1.0 | GPL v3 |
| SHORE | SHORE | Milou, Rackham, Irma, Bianca | 0.9.3 | GPL v3 |
| sickle | sickle | Milou, Rackham, Irma, Bianca | 1.210, 1.33-20-g4b0dc85-mullins | Other |
| SLiM | SLiM | Rackham, Irma, Bianca, Snowy | 3.2.1 | GPL v3 |
| snap | snap | Milou, Rackham, Irma, Bianca | 2013-02-16, 2013-11-29 | GPL |
| snippy | snippy | Milou, Rackham, Irma, Bianca | 4.0, 4.0.5 | GPL 2.0 |
| SNPTEST | SNPTEST | Rackham, Irma, Bianca, Snowy | 2.5.2, 2.5.5 | "As is" open source |
| SomaticSeq | SomaticSeq | Milou | 1.2.1 | Other |
| SPP | SPP | Rackham, Irma, Bianca, Snowy | 1.11 | GPL v2 |
| SRA Toolkit | sratools | Rackham, Irma, Bianca, Snowy | 2.3.5, 2.5.1, 2.5.7, 2.8.0, 2.8.2-1, 2.9.1-1 | Public domain |
| Stacks | Stacks | Rackham, Irma, Bianca, Snowy | 1.12, 1.19, 1.21, 1.22, 1.24, 1.29, 1.34, 1.35, 1.40, 1.48, 2.0Beta9, 2.0b, 2.2 | GPL v3 |
| strelka | strelka | Milou, Rackham, Irma, Bianca | 1.0.15 | GPL v3 |
| Strelka2 | Strelka2 | Milou, Rackham, Irma, Bianca | 2.8.4 | GPL v3 |
| Subread | subread | Milou, Rackham, Irma, Bianca | 1.4.5, 1.4.5-p, 1.5.0, 1.5.1, 1.5.2 | GPL |
| SVDetect | SVDetect | Milou | 0.8b | |
| SVMerge | SVMerge | Milou | 1.2r37 | Open source "as is" |
| svprops | svprops | Milou, Rackham, Irma, Bianca | 20171020-ebf6762 | GPL v3+ |
| tabix (includes bgzip) | tabix (Note: more recent versions in htslib module) | Milou, Rackham, Irma, Bianca | 0.2.6 | MIT/Expat |
| Tablet | Tablet | Milou, Rackham, Irma, Bianca | 1.15.09.01 | Custom "as is" redistributable |
| Tassel | Tassel | Milou | 3.0, 5.0 | |
| tbl2asn | tbl2asn | Milou, Rackham, Irma, Bianca | 25.3 | |
| TE-Tracker | TE-Tracker | Milou | 20141124 | |
| TEtools | TEtools | Milou, Rackham, Irma, Bianca | 1.0.0-283c1ca | GPL v3 |
| TIDDIT | TIDDIT | Milou, Rackham, Irma, Bianca | 2.3.0 | GPL v3 |
| transfuse | tranfuse | Milou, Rackham, Irma, Bianca | 0.5.0 | MIT |
| Transrate | transrate | Milou, Rackham, Irma, Bianca | 1.0.3 | MIT |
| TreeMix | TreeMix | Milou, Rackham, Irma, Bianca | 1.12 | GPL v3 |
| Trim Galore! | TrimGalore | Milou, Rackham, Irma, Bianca | 0.3.3, 0.3.7, 0.4.0, 0.4.1. 0.4.4 | GPL v3 |
| Trimmomatic | trimmomatic | Milou, Rackham, Irma, Bianca | 0.32, 0.36 | GPL |
| TSC | TSC | Milou, Rackham, Irma, Bianca | 1.2 | |
| UCSC Bioinformatics Utilities | ucsc-utilities | Milou, Rackham, Irma, Bianca | v287, v334, v345 | Other |
| UMI-tools | umi_tools | Rackham, Irma, Bianca | 0.5.3, 0.5.4 | MIT |
| usearch (32-bit version) | usearch | Milou, Rackham, Irma, Bianca | 5.2.236, 5.2.32, 6.1.544, 7.0.1090, 8.1.1861, 9.2.64 | Other |
| VarDictJava | VarDictJava | Milou, Rackham, Irma, Bianca | 1.4.5 | MIT |
| VarScan | VarScan | Milou, Rackham, Irma, Bianca | 2.3.6, 2.3.7, 2.4.2 | NPOSL |
| VAT | VAT | Milou, Rackham, Irma, Bianca | 2.0.1 | Other open-source |
| VCFaid | VCFaid | Milou, Rackham, Irma, Bianca | 20170616-f0732ae | GPL v3 |
| vcflib | vcflib | Milou, Rackham, Irma, Bianca | 2014-07-22 (milou only), 2016-08-29, 2017-04-04 | MIT |
| Variant Effect Predictor from Ensembl Tools | vep | Milou, Rackham, Irma, Bianca | 82, 84, 86, 87, 89, 91, 92 | Modified Apache |
| verifyBamID | verifyBamID | Rackham, Irma, Bianca | 1.1.2 | GPL v3, and others |
| ViennaRNA | RNAfold (ViennaRNA is an alias) | Milou, Rackham, Irma, Bianca | 1.8.4, 2.1.8, 2.2.5, 2.3.1 | Custom "as is" open source |
| vt | vt | Milou, Rackham, Irma, Bianca | 0.5772 | MIT |
| Bioinformatics Phylogeny | Module | Cluster | Version | License |
| beagle-lib | beagle | Milou, Rackham, Irma, Bianca | 1.0.0, 2.1.2 | GPL |
| BEAST | beast | Milou, Rackham, Irma, Bianca | 1.7.5, 1.8.1, 1.8.4 | GPL |
| BEAST2 | beast2 | Milou, Rackham, Irma, Bianca | 2.1.2, 2.3.1, 2.4.0, 2.4.8 | LGPL v2.1 |
| Concaterpillar | concaterpillar | Milou | 1.4, 1.8a | |
| CONSEL | CONSEL | Milou, Rackham, Irma, Bianca | 0.20 | |
| FastML | FastML | Milou, Rackham, Irma, Bianca | 3.1 | |
| FastTree | FastTree | Milou, Rackham, Irma, Bianca | 2.1.8, 2.1.10 | Open source "as is" |
| GARLI | garli | Milou, Rackham, Irma, Bianca | 2.1 | GPL v3 |
| Gubbins | gubbins | Milou, Rackham, Irma, Bianca | 1.4.2, 2.3.1 | GPL v2 |
| IQ-TREE | iqtree | Milou, Rackham, Irma, Bianca | 1.4.3-pomp, 1.5.3-omp, 1.5.4-omp-mpi, 1.6.5-omp-mpi, 1.6.10-omp-mpi | GPL v2 |
| MEGAN | MEGAN | Milou, Rackham, Irma, Bianca | 4.70.4, 5.1.5, 5.11.3, 6.3.5, 6.10.5 | Personal academic |
| MrBayes | mrbayes | Milou, Rackham, Irma, Bianca | 3.1.2-mpi, 3.2.20 (mpi), 3.2.1 (mpi), 3.2.3a (mpi), 3.2.4 (mpi), 3.2.6 (mpi), 3.2.6 with gcc 7.1.0 (mpi) | Public domain |
| NEXUS Class Library | ncl | Milou, Rackham, Irma, Bianca | 2.1.21-dev | Simplified BSD |
| PAML | paml | Milou, Rackham, Irma, Bianca | 4.6, 4.9e | Other |
| Phast | phast | Milou, Rackham, Irma, Bianca | 1.3, 1.4 | BSD |
| PhyloBayes | phylobayes | Milou, Rackham, Irma, Bianca | 4.1c | |
| PhyloBayes MPI | phylobayesmpi | Milou, Rackham, Irma, Bianca | 1.3b, 1.4f, 1.5a, 1.7a, 1.8 | GPL v2 |
| Phyutility | phyutility | Rackham, Irma, Bianca, Snowy | 2.7.3 | |
| RAxML | raxml | Milou, Rackham, Irma, Bianca | 7.0.4, 7.2.7, 7.2.8, 7.4.7, 8.0.20, 8.0.20-mpi, 8.2.0-gcc, 8.2.0-icc, 8.2.0-gcc-mpi, 8.2.0-icc-mpi, 8.2.4-gcc, 8.2.4-gcc-mpi, 8.2.10-gcc, 8.2.10-gcc-mpi | GPL |
| RAxML-NG | RAxML-NG | Rackham, Irma, Bianca, Snowy | 0.2.0b, 0.2.0b-mpi, 0.7.0b, 0.7.0b-mpi | GNU Affero GPL v3.0 |
| Bioinformatics Pipelines | Module | Cluster | Version | License |
| ab_wtp | ab_wtp | Milou | 1.1 (modified for SLURM) | GPL |
| bpipe | bpipe | Milou, Rackham, Irma, Bianca | 0.9.8.6, 0.9.8.7 | BSD |
| Bowtie | bowtie | Milou, Rackham, Irma, Bianca | 0.12.6, 0.12.7, 0.12.8, 0.12.9, 1.0.0, 1.0.1, 1.1.0, 1.1.2, 1.2.0 | Artistic |
| Bowtie2 | bowtie2 | Rackham, Irma, Bianca, Snowy | 2.0.0-beta5, 2.0.0-beta6, 2.0.2, 2.1.0, 2.2.3, 2.2.6, 2.2.9, 2.3.2, 2.3.3.1, 2.3.4.1, 2.3.4.3 | GPL v3 |
| Cluster Flow | clusterflow | Milou, Rackham, Irma, Bianca | 0.3, 0.4devel, 0.4 | GPL v3 |
| Cufflinks | cufflinks | Milou, Rackham, Irma, Bianca | 0.8.3, 0.9.1, 0.9.2, 0.9.3, 1.0.0, 1.0.1, 1.0.3, 1.1.0, 1.2.1, 1.3.0, 2.0.0, 2.0.2, 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 | MIT |
| fermikit | fermikit | Milou, Rackham, Irma, Bianca | r178, 0.14-prerelease-96f7820 | |
| HiC-Pro | HiC-Pro | Rackham, Irma, Bianca | 2.11.1 | BSD-3 |
| hichipper | hichipper | Rackham, Irma, Bianca | 0.7.3 | MIT |
| MIP | mip | Rackham, Irma, Bianca | 6.0.0 | MIT |
| Nextflow | Nextflow | Rackham, Irma, Bianca, Snowy | 18.10.1 | |
| Qiime | Qiime | Milou, Rackham | 1.4.0, 1.5.0, 1.6.0, 1.8.0, 1.9.1 | |
| qiime2 | qiime2 | Rackham, Irma, Bianca, Snowy | 2018.11.0 | BSD 3 |
| SMRT Link, SMRT Analysis | SMRT | Milou, Rackham, Irma, Bianca | 2.2.0, 2.3.0, 5.0.1 | |
| snakemake | snakemake | Milou, Rackham, Irma, Bianca | 3.10.1, 4.5.0 | |
| STAR | star | Milou, Rackham, Irma, Bianca | 2.3.0e, 2.3.1o, star/2.4.0f1, 2.4.1c, 2.4.2a, 2.5.0a, 2.5.0c, 2.5.1b, 2.5.2b, 2.5.3a | GPL v3 |
| STAR-Fusion | star-fusion | Milou, Rackham, Irma, Bianca | 1.0.0, 1.2.0 | Broad Institute redistributable as-is |
| Tophat | tophat | Milou, Rackham, Irma, Bianca | 1.0.14, 1.1.0, 1.1.3, 1.2.0, 1.3.3, 1.4.0, 2.0.0, 2.0.3, 2.0.4, 2.0.8b, 2.0.10, 2.0.11, 2.0.12, 2.1.1 | |
| Bioinformatics SW Collections | Module | Cluster | Version | License |
| 454-dataanalysis (Roche Newbler assembler) | 454-dataanalysis | Milou, Rackham, Irma, Bianca | 2.3, 2.53, 2.6, 2.9 | |
| 454-dataprocessing | 454-dataprocessing | Milou, Rackham, Irma, Bianca | 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 |
| BBMap | bbmap | Milou, Rackham, Irma, Bianca | 33.41, 35.14, 35.40, 37.53, 38.08 | Other |
| bcl2fastq | bcl2fastq | Milou, Rackham, Irma, Bianca | 1.8.3 (milou), 1.8.4, 2.15.0, 2.16.0, 2.17.1, 2.20.0 | |
| BEDOPS | BEDOPS | Milou, Rackham, Irma, Bianca | 2.4.3, 2.4.28 | GPL v2 |
| BEDTools | BEDTools | Milou, Rackham, Irma, Bianca | 2.10.0, 2.11.2, 2.16.2, 2.20.1, 2.21.0, 2.23.0, 2.25.0, 2.26.0, 2.27.1 | GPL |
| bioscope | bioscope | Milou | 1.2.1, 1.3.1 | Commercial |
| CASAVA | CASAVA | Milou, Rackham, Irma, Bianca | 1.7.0, 1.8.2 | |
| Chipster | chipster | Rackham, Irma, Bianca, Snowy | webstart | |
| Cell Ranger (Chromium 10X) | cellranger | Rackham, Irma, Bianca, Snowy | 1.1.0, 1.3.0, 2.0.2, 3.0.1 | other |
| EMBOSS | emboss | Milou | 6.3.1, 6.4.0, 6.5.7 | GPL |
| GATK | GATK | Milou, Rackham, Irma, Bianca | 1.0.4105, 1.0.5365, 1.2.12, 1.5.11, 1.5.21, 2.1.13, 2.3.6, 2.5.2, 2.7.2, 2.8.1, 3.1.1, 3.2.0, 3.2.2, 3.3.0, 3.4.0, 3.4.46, 3.5.0, 3.6, 3.7, 3.8-0, 4.beta.5
build-20160727 |
BSD Style |
| GATK-Queue | GATK-Queue | Milou, Rackham, Irma, Bianca | 3.2.2, 3.6, 3.7, 3.8-0 | MIT + academic non-commercial |
| GenomeSTRiP | GenomeSTRiP | Milou, Rackham, Irma, Bianca | 2.00.1650, 2.00.1685, 2.00.1710 | Custom 'as is' redistributable |
| HiSeq | HiSeq | Milou | 0.9 | |
| Long Ranger (Chromium 10X) | longranger | Milou, Irma, Rackham, Bianca | 2.0.1, 2.1.1, 2.1.2, 2.1.4 | other |
| MEME Suite | MEMEsuite | Milou | 4.11.1, 4.11.2_1 | BSD Style |
| SpeedSeq | SpeedSeq | Milou, Rackham, Irma, Bianca | 0.1.0-20151121, 0.1.2-20170504-30f8dc6 | MIT |
| Staden | staden | Milou | 2.0.0b6 | BSD |
| Supernova (Chromium 10X) | supernova | Milou, Rackham, Irma, Bianca | 1.0.0, 1.1.1, 1.1.4, 2.0.0 | other |
| VCFtools | vcftools | Milou, Rackham, Irma, Bianca | 0.1.8a, 0.1.11, 0.1.12, 0.1.13, 0.1.14, 0.1.15 | GPL |