Uppsala Multidisciplinary Center for Advanced Computational Science

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 that 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 Milou and Tintin, see the tutorial.

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

List of software

Software Module Cluster Version License
Compilers
Allinea DDT ddt Milou, Tintin, Rackham 3.2.1 Commercial
Ant ant Milou, Tintin, Irma, Rackham 1.8.1, 1.9.8, 1.10.0 Apache 2.0
Gnu binutils binutils Milou, Tintin 2.26 GPL v2, v3; LGPL v2, v3
CodeAnalyst CodeAnalyst Tintin 3.3
Cuda cuda Tintin 3.2, 4.1.28, 5.0
gcc gcc Milou, Tintin, Irma, Rackham 4.x, 5.x, 6.x gpl
Git git Milou, Tintin, Rackham 2.5.0, 2.10.2 LGPL 2.1
Guile guile Milou, Tintin 1.8.8 LGPL 2.1
intel intel Milou, Tintin, Irma, Rackham site license, 2 users
Java JDK java Milou, Tintin, Rackham 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

Other
Julia julia Milou, Tintin 0.3.0 pre-release MIT
LLVM llvm Milou, Tintin
Open64 open64 Milou, Tintin
patchelf patchelf Milou, Tintin 0.8 GPL v3
Perl perl Milou, Tintin, Irma, Rackham 5.18.2, 5.18.4 GPL, Perl
Perl Modules/Packages (large collection) perl_modules Milou, Tintin, Irma, Rackham 5.18.4 GPL, Perl
pgi pgi Milou, Tintin, Rackham site license, 5 users
Python python Milou, Tintin, Irma, Rackham 2.7.2, 2.7.6, 2.7.9, 2.7.11, 3.2, 3.2.4, 3.3, 3.3.1, 3.4.3, 3.5.0 GPL
Python 3 python3 Milou, Irma, Rackham 3.6.0 GPL
Ruby ruby Milou 2.0.0
Subversion subversion Milou, Tintin 1.9.3 Apache 2.0
SunStudio sunstudio Milou 12.1, 12.1u1
TotalView totalview Milou, Tintin 8.10.0-1, 8.8.0-2, 8.9.2-0, 8.9.2-2
Valgrind valgrind Milou 3.4.1
Chemistry/Physics
Gaussian
 
g03
g09
Milou, Tintin
g03.d02, g03.e01, g09.a02, g09.c01, g09.d01
UU site license
turbomole turbo Milou 6.1 user group license
gamess gamess Milou, Tintin 20110811R1 20101001R1 20070324R1 academic site license
VASP vasp Milou, Tintin 4.6.34, 5.2.8, 5.2.11, 5.2.12 user group license
molcas molcas Milou, Tintin 7.8.082, 8.0.15-03-08 user group license

gromacs

gromacs Milou, Tintin 4.5.5, 4.6.3, 4.6.5, 5.0.4 gpl

desmond

desmond Milou 2.2, 2.4, 2.4.2.1 gpl
nonmem nonmem Milou, Tintin 7.1.0, 7.1.2, 7.2.0, 7.3.0
Elmer elmer Tintin
MOLDEN molden Tintin 5.1
Engineering
Matlab matlab Milou, Tintin 7.10, 7.13, 7.4, 7.8, 8.0, 8.1, R2014a, R2015a, R2015b site license
envi envi Milou 4.8
openfoam openfoam Tintin 2.2.0
Comsom comsol Tintin, Milou 4.4 UU site license
Geospatial
GDAL GDAL Milou, Tintin 2.1.0 X/MIT style Open Source
GEOS GEOS Milou, Tintin 3.5.0 LGPL
libgeotiff libgeotiff Milou, Tintin 1.4.1 X-style and custom open-source "as is"
OpenFYBA / SOSI FYBA Milou, Tintin 4.1.1 Custom open-source "as is"
PROJ.4 PROJ.4 Milou, Tintin 4.9.2 MIT
Statistics
JAGS JAGS Milou, Tintin, Irma 4.2.0 GPL v2
R R Milou, Tintin, Irma, Rackham 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 GPL
R packages (modest collection) R_packages Milou, Tintin 3.3.0, 3.3.1
RStudio RStudio Milou, Tintin, Rackham system (milou), 1.0.136 (rackham) AGPL
stata stata Milou 12
Misc Applications
agrep agrep Milou, Tintin 3.41.5 ISC Open Source
Amazon Web Services Command Line Interface awscli Milou, Tintin 1.9.6 Apache 2.0
Circos circos Milou, Tintin 0.66
CMake cmake Milou, Tintin, Rackham 2.8.6 (Milou), 2.8.11.2 (Tintin default), 2.8.12.2 (Milou default), 3.5.1, 3.7.2 BSD 3-Clause
Cowsay cowsay Milou, Tintin 3.03 Artistic License
Doxygen doxygen Milou, Tintin 1.8.9.1, 1.8.11 Gnu GPL 2
GMT gmt Tintin 5.1.1
gnuplot gnuplot Milou, Tintin 4.4.3, 4.6.5
h5utils h5utils Milou, Tintin 1.12.1 GPL v2+
Haskell Tool Stack haskell-stack Milou, Rackham, Irma 1.0.4.3, 1.4.0 Custom "as is"
mbuffer mbuffer Milou, Tintin 20151002 GPL v3
MCL mcl Milou, Tintin 14-137 GPL v3
ROOT ROOT Milou, Tintin 6.04.08 LGPL v2.1
SCons SCons Milou, Tintin 2.5.0 misc free software
SWIG swig Milou, Tintin 3.0.7 GPL v3 plus some "as is"
SQLite sqlite Milou, Tintin (system), 3.8.5, 3.11.1, 3.16.2 Public domain
Texinfo texinfo Milou, Tintin 6.0 GPL v3
TeX Live texlive Milou, Rackham, Irma 2015, 2016 misc free software
tinyutils tinyutils Milou, Tintin 1.1, 1.2, 1.3 GPLv2
tmux tmux Tintin, Milou 1.9a
XZ Utils xz Milou, Tintin 5.2.2 Mixed
VIM vim Milou, Rackham, Irma 7.4-1941, 8.0-16 Custom
Parallel
mpjexpress mpjexpress Milou 0.38
intelmpi intelmpi Milou, Tintin, Irma, Rackham 5.1.2, 5.1.3, 17.0, 17.1, 17.2
openmpi openmpi Milou, Tintin, 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 Milou, Tintin, Rackham 20140222, 20170122 GPL
Libraries
ATLAS ATLAS Milou, Tintin 3.10.3 BSD-style
BLAS and CBLAS blas Milou, Rackham 3.6.0 Open source
Boost boost Milou, Tintin, Irma, Rackham 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 1.0.6 Custom open source "as is"
fftw fftw Milou 2.1.5, 3.2.2
FreeType freetype Milou, Rackham 2.6, 2.7.1 BSD-like FreeType and GPL v2
Gnu Scientific Library gsl Milou, Tintin, Rackham 1.16, 2.3 GPL
HDF4 hdf4 Milou, Tintin 4.2.11_gcc4.9.2 (built with gcc/4.9.2) BSD-style open source
HDF5 hdf5 Milou, Rackham 1.8.16_gcc4.9.2 (built with gcc/4.9.2), 1.8.18 (build with system gcc), 1.8.18_gcc6.3.0 (build with gcc/6.3.0 module) BSD-style open source
jemalloc jemalloc Milou, Tintin 3.6.0 BSD-derived
libcurl libcurl Milou, Tintin, Irma 7.45.0 Custom open source "as is"
libHaru libharu Milou, Tintin 2.3.0 ZLIB/LIBPNG License
NetCDF netcdf Milou (4.4.0), Tintin (4.3.0) 4.3.0_tintin_gcc, 4.3.0_tintin_intel, 4.4.0 Custom open source "as is"
OpenBLAS openblas Milou, Tintin, Rackham 0.2.14a, 0.2.19 BSD 3-clause
PCRE pcre Milou, Tintin 8.38 BSD 3-clause
Poppler Poppler Milou, Tintin 0.43.0 GPL v2
scalapack scalapack Milou 1.8.0
sparsehash sparsehash Milou, Irma, Rackham 2.0.2, 2.0.3
SZIP szip Milou, Rackham 2.1_gcc4.9.2 (built with gcc/4.9.2), 2.1.1 BSD-style open source
Intel Threading Building Blocks tbb Milou, Tintin 4.4u1_gcc4.9.2, 4.4u1_intel15.3 GPL v2
Yeppp Yeppp Milou, Tintin 1.0.0 Custom open source "as is"
zlib zlib Milou, Rackham 1.2.8 (default on milou), 1.2.11 ZLIB License
Bioinformatics Alignment Module Cluster Version License
ANFO anfo Milou 0.97, 0.98 GPL
Barrnap barrnap Milou, Rackham 0.2, 0.6, 0.8
Blasr and associated utilities blasr Milou 20150922, 5.3 Open source redistributable "as is"
BLAST (legacy) blast Milou, Tintin 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, Tintin, Rackham 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+ Public Domain
BLAT blat Milou, Tintin 34, 35 Other
BWA bwa Milou, Tintin, Irma, Rackham 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 GPL
bwa.kit bwakit Milou, Tintin 0.7.12 GPL
ClustalO clustalo Milou 1.2
ClustalW clustalw Milou, Tintin 2.1 LGPL
DIAMOND  diamond Milou, Tintin 0.7.9, 0.7.12, 0.8.26 Other open-source
Exonerate exonerate Milou, Rackham, Irma 2.2.0
FASTA fasta Milou, Tintin 36.3.6d (not Tintin), 36.3.6f, 36.3.8 Apache 2.0
GeneID geneid Milou 1.4.4 GPL
GMAP-GSNAP gmap-gsnap Milou, Tintin 2014-01-21, 2015-09-28, 2016-05-01 Custom as-is
HAL hal Milou, Tintin, Rackham 20151218, 20161130 open-source "as is" and others
HISAT2 HISAT2 Milou, Tintin 2.0.1-beta, 2.0.5 GPL
HMMER hmmer Milou, Rackham 2.3.2, 3.0, 3.1b1, 3.1b2 GPL
LASTZ lastz Milou 1.03.54
MAFFT MAFFT Milou, Tintin 7.205, 7.245 BSD (main), mixed open-source (extensions)
MafFilter MafFilter Milou, Tintin 1.1.2
mafTools mafTools Milou, Tintin 20141112 "As is" open source
Maq maq Milou 0.7.1 GPL
MOSAIK mosaik-aligner Milou, Tintin 1.0.1388, 1.1.0021, 2.2.3, 2.2.26 (incl. Tintin), 2.2.30 GPL
MPIBlast mpiblast Milou 1.6.0 GPL
Multiz multiz Milou, Tintin 012109
MUMmer MUMmer Milou, Tintin 3.22, 3.23 (default), 3.9.4alpha OSI
MUSCLE muscle Milou, Tintin 3.8.31, 3.8.1551 Public domain
Nextflow nextflow Milou, Irma 0.17.3, 0.22.2 GPLv3
NextGenMap NextGenMap Milou, Tintin 0.4.12 Artistic License 1.0
OMBlast OMBlast Milou, Tintin 1.0 unknown
OPTIMA optima Milou, Tintin f-1.3 GPL v2
pblat pblat Milou, Tintin 1.6 Same as blat
pblat-cluster pblat-cluster Milou 0.1 Same as blat
pfam_scan pfam_scan Milou 1.3, 1.5 GPL v3
PRANK prank Milou, Tintin 150803 GPL v2+
ProbCons ProbCons Milou, Tintin 1.12 Public domain
progressiveCactus progressiveCactus Milou, Tintin 2015-02-06, 2015-12-18, 2016-11-30 GPL v3, mostly
QualiMap QualiMap Milou, Tintin, Irma, Rackham 2.0.2, 2.2 GPL
RNAmmer rnammer Milou 1.2
SiBELia SiBELia Milou, Rackham 3.0.6
SortMeRNA SortMeRNA Milou, Tintin, Irma 2.1b GPL v3
SplitSeek splitseek Milou 1.3.2, 1.3.3, 1.3.4 GPL
Stampy Stampy Milou, Tintin 1.0.27 Custom (non-commercial)
T-Coffee T-Coffee Milou, Tintin 11.00.8cbe486 GPL v2
TRF trf Milou 4.07b
tRNAscan-SE tRNAscan-SE Milou 1.3.1 GPL
Vmatch Vmatch Milou, Tintin 2.2.5 Custom non-commercial
Vsearch vsearch Milou, Tintin 2.3.2 Dual GPL/BSD
Wise2 wise2 Milou, Tintin 2.2.0, 2.4.1 Other
Bioinformatics Annotation Module Cluster Version License
AAT AAT Milou r03052011
Augustus augustus Milou, Tintin 2.7, 3.0.1, 3.2.1, 3.2.2 Artistic License
Cegma cegma Milou 2.4.010312
Delly delly Milou 0.0.11, 0.3.3, 0.6.3, 0.7.2 GPL v3
GEMINI GEMINI Milou 0.16.3, 0.18.3, 0.19.0 MIT
HaMStR HaMStR Milou, Tintin 13.2.3 GNU GPL 3
InterProScan InterProScan Milou, Tintin 5.10-50.0, 5.11-51.0, 5.13-52.0, 5.15-54.0, 

5.20-59.0

Misc
MAKER maker Milou 2.28, 2.31, 2.31.6, 2.31.8 GPL
Scipio Scipio Milou 1.4 Custom non-commercial
SignalP SignalP Milou, Tintin 4.1 Custom academic user licence
snpEff snpEff Milou, Tintin, Irma 2.0.3, 2.0.5, 3.4, 3.6, 4.0, 4.1, 4.2 LGPL
TMHMM tmhmm Milou, Tintin 2.0c Custom academic as-is
TransDecoder TransDecoder Milou, Tintin 2.0.1 Broad Institute redistributable as-is
Trinotate trinotate Milou 2013-08-26, 2013-11-10, 2.0.1
Bioinformatics Assembly Module Cluster Version License
A5-MiSeq A5-miseq Milou, Tintin, Rackham 20140113, 20140604, 20160825 GPL
ABySS abyss Milou, Tintin, Irma 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 (also Tintin), 1.9.0-k128 (also Tintin) GPL v3
AllPathsLG allpathslg Milou, Irma 47300, 49618, 52485
AMOS AMOS Milou, Tintin 3.0.0, 3.1.0 Artistic
ARC assembler ARC_assembler Milou 1.1.3 Apache 2.0
BESST BESST Milou, Tintin 1.0.4.3, 1.0.4.4
CABOG (WGA assembler, Celera Assembler), includes PBcR cabog, CA (synonym) Milou, Tintin, Irma 8.1, 8.3 (also Tintin) GPL v2 and others for subcomponents
canu canu Milou, Tinti 1.0, 1.1, 1.3 GPL v2 and others for subcomponents
DBG2OLC DBG2OLC Milou, Tintin 20151208
DISCOVAR de novo DISCOVARdenovo Milou, Tintin 51885 Custom "as is"
FALCON FALCON Milou, Tintin 0.3.0, 0.4.1 Custom "as is"
FALCON-integrate FALCON-integrate Milou 20161113 Custom "as is"
fermi fermi Milou, Tintin 1.1-r751-beta
GARM GARM Milou, Tintin 0.7 (not Tintin), 0.7.3
IDBA IDBA Milou, Tintin 1.1.1 (max read length 128 bp), 1.1.1-384 (max 384 bp) GPL 2
MaSuRCA MaSuRCA Milou, Tintin, Irma 2.0.3.1 (Milou), 2.1.0 (Milou), 2.3.2, 3.1.3, 3.2.1
MEGAHIT megahit Milou, Tintin 1.0.3 GPL v3
MetAMOS MetAMOS Milou 1.5rc3 GPLv2 and other open source
Metassembler Metassembler Milou, Tintin 1.5 open-source
MHAP MHAP Milou, Tintin 1.6 Apache 2.0
Miniasm miniasm Milou 20160128 MIT
Minimap minimap Milou 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 15.8.24 Custom redistributable "as is"
Pilon Pilon Milou, Tintin 1.17 GPL v2
Platanus Platanus Milou, Tintin 1.2.1
Pmap pmap Milou 2010-11-25
RACA (Reference-Assisted Chromosome Assembly) RACA Milou, Tintin 0.9.1.1
Ray Ray Milou, Tintin 0.0.4, 0.0.7, 1.6.1, 2.3.0, 2.3.1 (Tintin), 2.3.1-mpiio (with support for MPI I/O, but this seems not to work very well) GPL
REAPR REAPR Milou 1.0.17 GPL
Redundans Redundans Milou, Rackham, Irma 0.13a-20170321 GPL v2
SGA SGA Milou 0.1.14 GPL v3
SOAPdenovo soapdenovo Milou, Irma 1.05, 2.04
SOAPdenovo-Trans soapdenovo-trans Milou, Tintin 1.03, 1.04 GPL v3
SPAdes spades Milou, Tintin, Irma, Rackham 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 GPL v3
StringTie StringTie Milou, Rackham, Irma 1.2.0, 1.3.3 Artistic
Trans-ABySS transabyss Milou 1.5.3 BCCA "As Is"
Trinity trinity Milou, Tintin, Irma 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 Other
Velvet velvet Milou 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
AdmixTools AdmixTools Milou 20160803, 5.0-20170312 Custom "as-is" open source
ADMIXTURE ADMIXTURE Milou, Tintin 1.3.0 Not open source
ALDER alder Milou, Tintin 1.03 Other
AlienTrimmer AlienTrimmer Milou 0.4.0 GPL
alleleCount allelleCount Milou, Rackham 2.2.0, 3.2.2 GPL
ANGSD ANGSD Milou, Tintin, Rackham 0.700, 0.902, 0.917 Open source
Artemis artemis Milou 15.0.0 GPL
Athlates Athlates Milou, Tintin 20140426 Custom
Bamtools bamtools Milou 2.3.0 MIT
BCFtools bcftools Milou, Tintin, Irma, Rackham 1.1, 1.2, 1.3, 1.3.1 MIT
BclConverter Bclconverter Milou 1.7.1
bgc bgc Milou, Tintin 1.03 GPL 3
Beagle beagle-app Milou 3, 4
BEETL BEETL Milou 1.0.2 BSD 2-Clause
BioPerl BioPerl Milou, Tintin, Rackham 1.6.1, 1.6.922, 1.6.923_Perl5.18.4, 1.6.924_Perl5.18.4 Perl
BioPython biopython Milou, Tintin, Rackham 1.56, 1.59, 1.64 (milou, tintin; loads python 2.7.6), 1.64-py3 (milou, tintin; loads python 3.3.1), 1.65 (milou; loads python 2.7.9), 1.65-py3 (milou; loads python/3.4.3); 1.68 (milou; loads python 2.7.6), 1.68-py3 (milou; loads python/3.4.3) Biopython
Bismark bismark Milou, Tintin, Irma, Rackham 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 GPL
BreakDancer breakdancer Milou, Tintin 1.4.4-u7, 1.4.5 (Tintin) GPL 3
BUSCO BUSCO Milou, Tintin 1.1b1, 1.2, 1.22 GPL v3+
CD-Hit aka cdhit cd-hit Milou, Tintin 4.6.1, 4.6.4 GPL v2
Cell Profiler cellprofiler Milou 2.1.0
CleaveLand4 CleaveLand4 Milou, Tintin 4.3 GPL v3
cnD cnD Milou, Tintin 1.3 GPL 3
CNV-seq CNV-seq Milou, Tintin 20140812 Misc open source
CNVnator CNVnator Milou, Tintin 0.3, 0.3.2 Creative Commons Public License
Corset Corset Milou, Tintin 1.04 GPL v3
CRAM Tools cramtools Milou 2.0
deepTools deepTools Milou, Tintin 1.5.11 (milou only), 2.0.1, 2.2.3, 2.3.1 GPL v3
DWGSIM DWGSIM Milou, Tintin 0.1.11-6e9a361 GPL v2
EEMS eems Milou 20060605 Misc open source
EIGENSOFT eigensoft Milou, Tintin, Rackham 4.2, 5.0.1, 6.0.1 (long ID support), 6.1.2 (default ID), 6.1.4 (long ID support) Custom
EMIRGE emirge Milou 0.60 GPL
EMMAX emmax Milou Beta-07Mar2010 GPL
EnsEMBL Perl API EnsEMBL-API Milou, Tintin 87 Modified Apache
EPACTS EPACTS Milou, Tintin 3.2.6 GPL v3
eXpress eXpress Milou, Tintin 1.5.1 Artistic License 2.0
FastQC FastQC Milou, Tintin 0.6.1, 0.7.2, 0.10.1, 0.11.1, 0.11.2, 0.11.5 GPL
fastq_screen fastq_screen Milou 0.3.1, 0.4.3. 0.5.1, 0.9.2 GPL
FASTX Fastx Milou 0.0.13, 0.0.14 AGPLv3
FLASH FLASH Milou, Tintin 1.2.11 GPL
flashpca flashpca Milou 1.1.2.1 GPL
FreeBayes freebayes Milou, Tintin 0.8.9, 0.9.4, 0.9.4_2012-04-16, 0.9.8, 0.9.21, 1.0.2 MIT
FusionCatcher FusionCatcher Milou 0.99.3e, 0.99.5a GPL
GAM-NGS gam-ngs Milou, Tintin 1.1b GPL
GCTA gcta Milou 0.92.0, 0.92.6, 0.93.9 Public domain
GEM GEM Milou, Tintin, Irma 2.7 "Research only"
GeneMark GeneMark Milou 2.3-es Other
GenomeTools GenomeTools Milou, Tintin 1.3.5 (Milou), 1.5.8 BSD style
GERP++ GERP++ Milou, Tintin 20110522 GPL v3+
GTOOL GTOOL Milou, Tintin 0.7.5 "As is" open source
GCTA gcta Milou, Rackham 0.92.0, 0.92.6, 0.93.9, 1.26.0 MIT
gvcftools gvcftools Milou, Tintin 0.16.2, 0.17.0 Various "As Is" open source
HTSlib htslib Milou, Tintin, Rackham 1.2.1, 1.3, 1.3.2 MIT
HTSeq htseq Milou 0.4.6, 0.5.1. 0.6.1 GPL
Integrative Genomics Viewer IGV Milou, Tintin 1.5.51, 2.3.17, 2.3.40 (Tintin) LGPL
Integrative Genomics Viewer Tools IGVtools Milou, Tintin 2.2.1, 2.3.17, 2.3.40 (Tintin) LGPL
IM IM Milou 20091217
IMa2p IMa2p Milou, Tintin 2015-08-09 GPL v3
IMPUTE2 IMPUTE2 Milou, Tintin 2.3.2 "As is" open source
ITSx ITSx Milou 1.0.9 GPL
Jellyfish jellyfish Milou, Tintin 1.1.11 (no Tintin), 2.0.0 (no Tintin), 2.1.4, 2.2.3-dev, 2.2.4 GPL
kallisto kallisto Milou, Tintin 0.42.4, 0.43.0 UC Regents "As Is"
KAT KAT Milou, Tintin 2.0.4, 2.0.6, 2.0.8, 2.1.1 GPL v3
KmerGenie KmerGenie Milou, Tintin 1.6741 Other
Kraken Kraken Milou, Tintin 0.10.5-beta GPL v3
Krona Krona Milou, Tintin 2.7 Custom open source
LASER LASER Milou, Tintin 2.01, 2.02 GPL v3
Latent Strain Analysis LatentStrainAnalysis Milou 20160322 (fork of a fork) MIT
LDhelmet LDhelmet Milou, Tintin 1.7 GPL
liftOver liftOver Milou, Rackham 2017-03-14
LTR Finder ltr-finder Milou 1.0.5
LUMPY LUMPY Milou 0.2.12 MIT
MACS MACS Milou 1.4.1, 1.4.2, 2.1.0 Other
MACE MACE Milou, Tintin, Irma 1.2
manta manta Milou, Tintin 0.27.1, 1.0.0, 1.0.3 GPL v3
mapDamage mapDamage Milou 2015-04-10 Public Domain
matrix2png matrix2png Milou 1.2.1 Apache
Meerkat Meerkat Milou 0.189 Misc non-commercial open source
MetaBAT MetaBat Milou, Tintin 0.26.3 BSD-like
Metaxa2 Metaxa2 Milou, Tintin 2.1.3 GPL v3
micca micca Milou 1.4.0 GPL v3
Mimar mimar Milou 20101217
miRDeep2 mirdeep2 Milou 2.0.0.5
MMSEQ mmseq Milou, Tintin 1.0.8a GPL
Mothur Mothur Milou, Tintin 1.30.1, 1.33.3 (MPI support), 1.36.1 (incl. Tintin), 1.38.1 GPL v3
MSMC msmc Milou 2014-09-29, 0.1.0 GPL
MultiQC MultiQC Milou, Tintin, Rackham 0.3.1, 0.3.1-py3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9 MIT
MuTect mutect Milou 1.1.5 Other
ngsplot ngsplot Milou 2.61 GPL v2
NGSrich ngsrich Milou 0.7.8
NGSUtils NGSUtils Milou, Tintin 0.5.9 Custom open source "as is"
OpenMS OpenMS Milou 2.0.0 BSD + other
OrthoMCL OrthoMCL Milou 2.0.9
PEAR pear Milou 0.9.5, 0.9.10 CC
PennCNV PennCNV Milou, Tintin 20151014 Public domain
Pftools pftools Milou, Tintin 2.3
phantompeakqualtools phantompeakqualtools Milou 1.1 MIT
Picard picard Milou, Tintin, Irma 1.40, 1.41, 1.59, 1.64, 1.69, 1.85, 1.92, 1.114, 1.118 (also Tintin starting here), 1.119, 1.127, 1.141, 2.0.1 MIT
Pindel pindel Milou, Tintin 0.2.4w GPL 3
PLINK plink Milou 1.07, 1.90
PLINK/SEQ plinkseq Milou 0.08 (formerly mislabelled as 0.8), 0.10 Other
Poretools poretools Milou, Tintin 0.5.1-devel Open source
Preseq preseq Milou 0.1.0 GPL
Primer3 Primer3 Milou 2.3.7 GPL v2
PSORTb psortb Milou 3.0 GPL
Pysam pysam Milou, Rackham 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 MIT
qctool qctool Milou, Tintin 1.4 "As is" open source
QuantiSNP QuantiSNP Milou, Tintin 2.2
QUAST quast Milou, Tintin 2.2, 2.3, 3.2
QuorUM QuorUM Milou, Tintin 1.0.0 GPL v3
RDXplorer RDXplorer Milou 3.2 open source
RepeatMasker RepeatMasker Milou, Rackham 3.3.0, 4.0.1, 4.0.6, 4.0.7 open source
RepeatModeler RepeatModeler Milou, Rackham 1.0.7, 1.0.8, 1.0.8_RM4.0.7 open source
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 2.3, 2.3.6, 2.3.9, 2.4, 2.6.1
RTG Tools rtgtools Milou, Tintin, Irma 3.7.1 BSD
Sailfish Sailfish Milou 0.8.0 GPL v3+
Salmon Salmon Milou, Tintin 0.6.0 GPL v3+
sambamba sambamba Milou, Tintin 0.5.9 GPL v2+
samblaster samblaster Milou, Tintin 0.1.22 MIT
samplefq samplefq Milou, Tintin 0.2 GPL v3
SAMtools samtools Milou, Tintin, Irma, Rackham 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 MIT
SBT (bloomtree) SBT Milou, Tintin 0.1, 0.3
Scalpel scalpel Milou, Tintin 0.5.2 MIT
Schmutzi schmutzi Milou 20160424
SCORE-Seq SCORE-Seq Milou, Tintin 5.3
Selscan selscan Milou, Tintin 1.1.0 GPL v3
SeqAn SeqAn Milou 1.4.2 Other open-source
seqMINER seqMINER Milou, Tintin 1.3.3e
SeqTK seqtk Milou, Tintin 1.0-r31, 1.0-r68e, 1.0
SeqMonk seqmonk Milou, Tintin 0.21.0, 0.27.0, 0.32.1 (also tintin), 0.34.1, 1.36.0 GPL
SeqPrep SeqPrep Milou 2013-11-14 Public domain
SeqTools SeqTools Milou 4.20
SHAPEIT SHAPEIT Milou, Tintin v2.r837 Custom non-commercial
SHORE SHORE Milou 0.9.3 GPL v3
sickle sickle Milou 1.210 Other
snap snap Milou 2013-02-16 GPL
SNPTEST SNPTEST Milou, Tintin 2.5.2 "As is" open source
soapcorrector soapcorrector Milou 1.0
SomaticSeq SomaticSeq Milou 1.2.1 Other
SPP SPP Milou 1.11
SRAToolkit sratools Milou, Tintin 2.3.5, 2.5.1, 2.5.7, 2.8.0 Public domain
Stacks Stacks Milou, Tintin 1.12, 1.19, 1.21, 1.22, 1.24, 1.29, 1.34, 1.35, 1.40 GPL v3
strelka strelka Milou, Tintin 1.0.15 GPL v3
Subread subread Milou, Tintin, Rackham 1.4.5 (only Milou), 1.4.5-p1 (only Milou), 1.5.0, 1.5.1, 1.5.2 GPL
SVDetect SVDetect Milou, Tintin 0.8b
SVMerge SVMerge Milou 1.2r37 Open source "as is"
tabix (includes bgzip) tabix Milou, Tintin 0.2.6
Tablet Tablet Milou, Tintin 1.15.09.01 Custom "as is" redistributable
Tassel Tassel Milou, Tintin 3.0, 5.0
TE-Tracker TE-Tracker Milou, Tintin 20141124
TreeMix TreeMix Milou, Tintin 1.12 GPL v3
Transrate transrate Milou, Tintin 1.0.3 MIT
Trim Galore! TrimGalore Milou, Tintin 0.3.3, 0.3.7, 0.4.0, 0.4.1 GPL v3
Trimmomatic trimmomatic Milou, Irma, Rackham 0.32, 0.36 GPL
TSC TSC Milou, Tintin 1.2
UCSC Bioinformatics Utilities ucsc-utilities Milou, Rackham, Irma v287, v334, v345 (latter two only Milou) Other
usearch usearch Milou, Tintin 5.2.236, 5.2.32, 6.1.544, 7.0.1090, 8.1.1861 Other
VarDictJava VarDictJava Milou 1.4.5 MIT
VarScan VarScan Milou 2.3.6, 2.3.7 NPOSL
VAT VAT Milou, Tintin 2.0.1 Other open-source
vcflib vcflib Milou, Tintin 2014-07-22 (milou only), 2016-08-29 MIT
Variant Effect Predictor from Ensembl Tools vep Milou 82, 84 Modified Apache
ViennaRNA RNAfold (ViennaRNA is an alias) Milou, Tintin 1.8.4, 2.1.8, 2.2.5, 2.3.1 Custom "as is" open source
vt vt Milou, Tintin, Rackham 0.5772 MIT
Bioinformatics Phylogeny Module Cluster Version License
beagle-lib beagle Milou, Tintin 1.0.0, 2.1.2, 2.1.2-gpu GPL
BEAST beast Milou, Tintin 1.7.5, 1.8.1 GPL
BEAST2 beast2 Milou, Tintin 2.1.2, 2.3.1, 2.4.0 LGPL v2.1
Concaterpillar concaterpillar Milou, Tintin 1.4, 1.8a
FastML FastML Milou, Tintin 3.1
FastTree FastTree Milou, Tintin 2.1.8 Open source "as is"
GARLI garli Milou, Tintin 2.1 GPL v3
Gubbins gubbins Milou 1.4.2 GPL v2
IQ-TREE iqtree Milou, Rackham 1.4.3-pomp, 1.5.3-omp GPL v2
MEGAN MEGAN Milou 4.70.4, 5.1.5, 5.11.3, 6.3.5 Personal academic
MrBayes mrbayes Milou, Tintin 3.1.2-mpi, 3.2.20 (mpi), 3.2.1 (mpi), 3.2.3a (mpi/gpu), 3.2.4 (mpi/gpu), 3.2.6 (mpi/gpu) Public domain
NEXUS Class Library ncl Milou, Tintin 2.1.21-dev Simplified BSD
PAML paml Milou 4.6 Other
Phast phast Milou, Tintin, Rackham 1.3, 1.4 (tintin) BSD
phylobayesmpi phylobayesmpi Milou 1.3b, 1.4f, 1.5a, 1.7a
RAxML raxml Milou, Tintin 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 GPL
Bioinformatics Pipelines Module Cluster Version License
ab_wtp ab_wtp Milou 1.1 (modified for SLURM) GPL
bpipe bpipe Milou 0.9.8.6, 0.9.8.7 BSD
Bowtie bowtie Milou, Tintin, Irma 0.12.6, 0.12.7, 0.12.8, 0.12.9, 1.0.0, 1.0.1, 1.1.0, 1.1.2 Artistic
Bowtie2 bowtie2 Milou, Tintin, Irma 2.0.0-beta5, 2.0.0-beta6, 2.0.2, 2.1.0, 2.2.3, 2.2.6, 2.2.9 GPL
Cluster Flow clusterflow Milou, Irma 0.3, 0.4devel, 0.4 GPL v3
Cufflinks cufflinks Milou, Irma 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 Other
cutadapt cutadapt Milou, Tintin, Irma 1.2.1, 1.3, 1.4.2, 1.5.0. 1.8.0, 1.9.1 Public domain
Qiime Qiime Milou, Rackham 1.4.0, 1.5.0, 1.6.0, 1.8.0, 1.9.1
STAR star Milou, Tintin, Rackham 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 GPL v3
Tophat tophat Milou, Tintin, Irma 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
Bioinformatics SW Collections Module Cluster Version License
454-dataanalysis (Roche Newbler assembler) 454-dataanalysis Milou, Tintin 2.3, 2.53, 2.6, 2.9 (only version on Tintin)
454-dataprocessing 454-dataprocessing Milou 2.3
ANNOVAR annovar Milou

2011.02.20, 2011.05.06, 2012.02.23, 2012.05.25, 2013.09.12, 2014.07.14, 2014.11.12, 2015.06.17, 2016.05.11

Other
BBMap bbmap Milou, Tintin 33.41, 35.14, 35.40 Other
bcl2fastq bcl2fastq Milou, Nestor, Tintin 1.8.3, 1.8.4, 2.15.0 (here and earlier, Milou only), 2.16.0 (all systems), 2.17.1
BEDOPS BEDOPS Milou, Tintin 2.4.3 GPL v2
BEDTools BEDTools Milou, Tintin, Rackham 2.10.0, 2.11.2, 2.16.2, 2.20.1, 2.21.0, 2.23.0, 2.25.0, 2.26.0 GPL
bioscope bioscope Milou 1.2.1, 1.3.1 Commercial
CASAVA CASAVA Milou 1.7.0, 1.8.2
chipster chipster Milou webstart
Cell Ranger (Chromium 10X) cellranger Milou, Irma 1.1.0 other
EMBOSS emboss Milou, Tintin 6.3.1, 6.4.0, 6.5.7 GPL
GATK GATK Milou, Tintin, Irma 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

build-20160727

BSD Style
GATK-Queue GATK-Queue Milou, Tintin, Irma 3.2.2, 3.6, 3.7 MIT + academic non-commercial
GenomeSTRiP GenomeSTRiP Milou, Rackham 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 2.0.1, 2.1.1, 2.1.2 other
MEME Suite MEMEsuite Milou 4.11.1, 4.11.2_1 BSD Style
SMRT SMRT Milou 2.2.0, 2.3.0
SpeedSeq SpeedSeq Milou 0.1.0-20151121 MIT
Staden staden Milou 2.0.0b6 BSD
Supernova (Chromium 10X) supernova Milou, Irma 1.0.0, 1.1.1 other
VCFtools vcftools Milou, Tintin 0.1.8a, 0.1.11, 0.1.12, 0.1.13, 0.1.14 GPL