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Software

Category Name Module Cluster Versions Licence
Alignment blast blast rackham bianca miarka snowy 2.14.1+, 2.15.0+ Public Domain
Alignment bowtie2 bowtie2 rackham bianca miarka snowy 2.5.2 GPL v3
Alignment cactus cactus rackham bianca miarka snowy 2.7.2, 2.8.2 Copyright
Alignment ClipKIT ClipKIT rackham bianca miarka snowy 2.2.4 MIT
Alignment CrossMap CrossMap rackham bianca miarka snowy 0.6.6 GPL v2+
Alignment diamond diamond rackham bianca miarka snowy 2.0.6, 2.1.9 GPL v3
Alignment fasta fasta rackham bianca miarka snowy 36.3.8i Apache 2.0
Alignment hmmer hmmer rackham bianca miarka snowy 3.4 custom open-source
Alignment last last rackham bianca miarka snowy 1505 None
Alignment lastz lastz rackham bianca miarka snowy 1.04.22 MIT
Alignment mapAD mapAD rackham bianca miarka snowy 0.42.1 MIT
Alignment mapcaller mapcaller rackham bianca miarka snowy 0.9.9.41 MIT
Alignment MashMap MashMap rackham bianca miarka snowy 3.0.4 Mixed
Alignment minimap2 minimap2 rackham bianca miarka snowy 2.26-r1175 MIT
Alignment miniprot miniprot rackham bianca miarka snowy 0.12, 0.13 MIT
Alignment MMseqs2 MMseqs2 rackham bianca miarka snowy 14-7e284, 15-6f452 GPL v3
Alignment ngmlr ngmlr rackham bianca miarka snowy 0.2.7-20210816-a2a31fb MIT
Alignment pbmm2 pbmm2 rackham bianca miarka snowy 1.13.0 BSD 3
Alignment randfold randfold rackham bianca miarka snowy 2.0.1 None
Alignment RMBlast RMBlast rackham bianca miarka snowy 2.2.28, 2.14.1+ Public domain
Alignment skani skani rackham bianca miarka snowy 0.2.1 MIT
Alignment SNAP-aligner SNAP-aligner rackham bianca miarka snowy 2.0.3 Apache 2.0
Alignment spaln spaln rackham bianca miarka snowy 3.0.3 GPL v2 and custom
Alignment star star rackham bianca miarka snowy 2.7.8a, 2.7.11a MIT
Alignment trf trf rackham bianca miarka snowy 4.10.0-rc.2 Gnu Afferoo GPL v3
Alignment US-align US-align rackham bianca miarka snowy 20230727-e5c6270 Custom open source AS-IS
Alignment wfmash wfmash rackham bianca miarka snowy 0.12.5 MIT
Annotation af2complex af2complex rackham bianca miarka snowy 1.4.0 None
Annotation alphapulldown alphapulldown rackham bianca miarka snowy 1.0.4 GPL-3.0
Annotation augustus augustus rackham bianca miarka snowy 3.5.0, 3.5.0-20231223-33fc04d Artistic License 1.0
Annotation bali-phy bali-phy rackham bianca miarka snowy 4.0-beta15 None
Annotation bcftools-score bcftools-score rackham bianca miarka snowy 1.18-20231207-9c8e21e MIT
Annotation braker braker rackham bianca miarka snowy 3.0.3, 3.0.7, 3.0.8 Artistic 1.0
Annotation colabfold-local colabfold-local rackham bianca miarka snowy 1.5.5 MIT
Annotation compleasm compleasm rackham bianca miarka snowy 0.2.2, 0.2.5, 0.2.6 Apache 2.0 and others
Annotation CookHLA CookHLA rackham irma bianca miarka snowy 1.0.0 None
Annotation DeepLoc DeepLoc rackham bianca miarka snowy 2.0 None
Annotation dorado dorado rackham bianca miarka snowy 0.6.1, 0.8.2 PLC 1.0
Annotation duplex-tools duplex-tools rackham bianca miarka snowy 0.3.3 MPL 2.0
Annotation funannotate funannotate rackham bianca miarka snowy 1.8.1, 1.8.17 BSD-2
Annotation GeneMark GeneMark rackham bianca miarka snowy 4.69-es, 4.71-es, 4.72-es Custom
Annotation GeneMark-ETP GeneMark-ETP rackham bianca miarka snowy 1.02-20231213-dd8b37b Creative Commons Attribution NonCommercial ShareAlike 4.0 License
Annotation GenomeThreader GenomeThreader rackham bianca miarka snowy 1.7.4 Custom AS IS
Annotation HATCHet HATCHet rackham bianca miarka snowy 2.0.1 BSD-3
Annotation HATK HATK rackham bianca miarka snowy 2.0beta AS IS
Annotation hybpiper hybpiper rackham bianca miarka snowy 2.1.6 GPLv3
Annotation igv-reports igv-reports rackham bianca miarka snowy 1.12.0-python3.9.5 MIT
Annotation InterProScan None None 5.65-97.0, 5.67-99.0, .z None
Annotation IsoQuant IsoQuant rackham bianca miarka snowy 3.3.1 Custom
Annotation jcvi jcvi rackham bianca miarka snowy 1.3.8 BSD2
Annotation kmersGWAS kmersGWAS rackham irma bianca miarka snowy 20221010-a706bb7 None
Annotation LDAK LDAK rackham bianca miarka snowy 5.2 Open source AS IS
Annotation LOHHLA LOHHLA rackham bianca miarka snowy 20210129-00744c5 None
Annotation LOHHLA-slagtermaarten LOHHLA-slagtermaarten rackham bianca miarka snowy 20200219-b38c477 None
Annotation macse macse rackham bianca miarka snowy 2.07 None
Annotation MakeHub MakeHub rackham bianca miarka snowy 1.0.5-20200210-1ecd6bb, 1.0.8-20240217-31cc299 GPL v3
Annotation metaeuk metaeuk rackham bianca miarka snowy 6-a5d39d9 GPL v3
Annotation OBITools OBITools rackham bianca miarka snowy 1.2.13 CeCILL
Annotation OBITools3 OBITools3 rackham bianca miarka snowy 3.0.1b24 CeCILL
Annotation omm-macse omm-macse rackham bianca miarka snowy 12.01 None
Annotation ORFfinder ORFfinder rackham irma bianca miarka snowy 0.4.3 Public domain
Annotation OrthoFinder OrthoFinder rackham bianca miarka snowy 2.5.2, 2.5.5 GPL v3
Annotation polysolver polysolver rackham bianca miarka snowy v4 None
Annotation ProtHint ProtHint rackham bianca miarka snowy 2.6.0-20231027-103304c GeneMark license
Annotation pullseq pullseq rackham bianca miarka snowy 20230518-7381691 None
Annotation pVACtools pVACtools rackham bianca miarka snowy 3.1.1 BSD3
Annotation pycoQC pycoQC rackham bianca miarka snowy 2.5.2 GPL-3.0
Annotation RepeatMasker RepeatMasker rackham bianca miarka snowy 4.1.5 None
Annotation sepp sepp rackham bianca miarka snowy 4.3.10_python_3.7.2, 4.5.1, 4.5.2 GPL v3
Annotation sequenza-utils sequenza-utils rackham bianca miarka snowy 3.0.0 None
Annotation SignalP SignalP rackham bianca miarka snowy 6.0h None
Annotation snpEff snpEff rackham bianca miarka snowy 5.2 MIT
Annotation soprano soprano rackham bianca miarka snowy 20240418-938604e GPL-3.0
Annotation svtools svtools rackham bianca miarka snowy 0.5.1 MIT
Annotation tabixpp tabixpp rackham bianca miarka snowy 1.1.2 MIT
Annotation TEspeX TEspeX rackham bianca miarka snowy 2.0.1 GPL v3
Annotation TransDecoder TransDecoder rackham bianca miarka snowy 5.7.1-20230913-8b926ac None
Annotation TrEMOLO TrEMOLO rackham bianca miarka snowy 2.2-beta1 GPL v3
Annotation trex trex rackham bianca miarka snowy 20230904-df86afe, 20231120-d9c840a None
Annotation TSEBRA TSEBRA rackham bianca miarka snowy 1.1.2.4 Artistic License 2.0
Annotation vartrix vartrix rackham bianca miarka snowy 1.1.22 MIT
Annotation vcf2maf vcf2maf rackham bianca miarka snowy 1.6.21 Apache 2.0
Annotation WhatsHap WhatsHap rackham bianca miarka snowy 2.3-20240529-be88057 MIT
Assembly assembly-stats assembly-stats rackham bianca miarka snowy 1.0.1-20211102-c006b9c GPL v3
Assembly GetOrganelle GetOrganelle rackham bianca miarka snowy 1.7.3.3, 1.7.7.0 GPLv3
Assembly hifiasm hifiasm rackham bianca miarka snowy 0.16.1-r375, 0.19.8-r603, 0.20.0-r639 MIT
Assembly hifiasm-meta hifiasm-meta rackham bianca miarka snowy 0.3.2-r74 MIT
Assembly IPA IPA rackham irma bianca miarka snowy 1.8.0 BSD 3-clause
Assembly L_RNA_scaffolder L_RNA_scaffolder rackham bianca miarka snowy 20190530-98f19e3 None
Assembly MBG MBG rackham bianca miarka snowy 1.0.14 MIT
Assembly metaMDBG metaMDBG rackham bianca miarka snowy 0.3-20240117-57f4493 MIT
Assembly miniasm miniasm rackham bianca miarka snowy 0.3-r179-20191007-ce615d1 MIT
Assembly Polypolish Polypolish rackham bianca miarka snowy 5.0 GPL-3.0
Assembly purge_dups purge_dups rackham bianca miarka snowy 1.2.5, 1.2.6 MIT
Assembly Redundans Redundans rackham bianca miarka snowy 2.0.1 GPL v3
Assembly shovill shovill rackham bianca miarka snowy 1.0.0, 1.1.0 GPL-3.0
Assembly SKESA SKESA rackham bianca miarka snowy 2.4.0 Public domain
Assembly spades spades rackham bianca miarka snowy 4.0.0 GPL v2
Assembly StringTie StringTie rackham bianca miarka snowy 2.2.1 MIT
Assembly Trycycler Trycycler rackham bianca miarka snowy 0.5.4 GPL-3.0
Assembly vg vg rackham bianca miarka snowy 1.29.0, 1.48.0 mixed
Bioinformatics alignment AGE AGE bianca irma milou rackham snowy 0.4 None
Bioinformatics alignment GEM-Tools GEM-Tools rackham irma bianca snowy 1.7.1 None
Bioinformatics alignment HISAT2 HISAT2 bianca irma rackham snowy 2.0.1-beta, 2.0.5, 2.1.0, 2.2.1 GPL v3
Bioinformatics alignment infernal infernal bianca miarka milou rackham snowy 1.0.2, 1.1.1, 1.1.2 BSD
Bioinformatics alignment Kalign Kalign rackham irma bianca snowy 1.04, 2.04 None
Bioinformatics alignment LEON-BIS LEON-BIS bianca irma milou rackham snowy 20130322 None
Bioinformatics alignment MafFilter MafFilter bianca irma milou rackham snowy 1.1.2 None
Bioinformatics alignment MAFFT MAFFT bianca irma rackham snowy 7.205, 7.245, 7.310, 7.407 BSD (main), mixed open-source (extensions)
Bioinformatics alignment MUMmer MUMmer rackham irma bianca snowy 3.9.4alpha, 3.22, 3.23, 4.0.0beta2, 4.0.0rc1 Artistic License 2.0
Bioinformatics alignment unimap unimap rackham irma bianca snowy 0.1-r46-dirty MIT
Bioinformatics annotation AAT AAT bianca irma milou rackham snowy r03052011 Custom "AS IS"
Bioinformatics annotation GEMINI None None 0.16.3, 0.18.3, 0.19.0, 0.20.0, 0.20.1, .gemini_0.18.3 None
Bioinformatics annotation HaMStR None None 13.2.3, .HaMStR, .HaMStR-old None
Bioinformatics annotation InterProScan InterProScan bianca miarka rackham snowy 5.52-86.0 Misc
Bioinformatics annotation libBigWig libBigWig rackham irma bianca snowy 0.4.4 MIT
Bioinformatics annotation ProtHint ProtHint rackham miarka bianca snowy 2.4.0 GeneMark license https://github.com/gatech-genemark/ProtHint/blob/master/LICENSE
Bioinformatics annotation tmhmm tmhmm rackham miarka bianca snowy 2.0c Custom as-is
Bioinformatics annotation VIBRANT VIBRANT rackham irma bianca snowy 1.2.1 GNU General Public License
Bioinformatics assembly A5-miseq None None 20140113, 20140604, 20160825, .A5-miseq None
Bioinformatics assembly abyss abyss bianca irma milou rackham snowy 1.3.5, 1.3.5-max, 1.3.7, 1.3.7-k128, 1.3.7-max, 1.5.2, 1.9.0, 1.9.0-k128, 2.0.2, 2.0.2-k128 GPL v3
Bioinformatics assembly allpathslg None bianca irma rackham snowy 47300, 49618, 52485, 52488 None
Bioinformatics assembly AMOS AMOS bianca irma milou rackham snowy 3.0.0, 3.1.0 Artistic
Bioinformatics assembly ARC_assembler ARC_assembler milou 1.1.3 Apache 2.0
Bioinformatics assembly ARCS ARCS rackham irma bianca snowy 1.0.6, 1.1.1 GPL v3
Bioinformatics assembly BESST None None 1.0.4.3, 1.0.4.4, .besst None
Bioinformatics assembly DBG2OLC DBG2OLC rackham snowy miarka bianca 20151208 None
Bioinformatics assembly DISCOVARdenovo None bianca miarka rackham snowy 51885, 52488 None
Bioinformatics assembly FALCON FALCON rackham miarka bianca snowy 0.3.0, 0.4.1, 2018.31.08-03.06 Clear BSD
Bioinformatics assembly FALCON-integrate FALCON-integrate bianca miarka milou rackham snowy 20161113 Custom "as is"
Bioinformatics assembly Flye Flye rackham miarka bianca snowy 2.3.5, 2.4.2, 2.8.1 -d
Bioinformatics assembly GAA GAA rackham miarka bianca snowy 1.1 GPL v2+
Bioinformatics assembly GARM GARM bianca irma milou rackham snowy 0.7, 0.7.3 None
Bioinformatics assembly IDBA None bianca miarka rackham snowy 1.1.1, 1.1.1-384, 1.1.3 None
Bioinformatics assembly LINKS LINKS rackham miarka bianca snowy 1.8.7 GPL v3
Bioinformatics assembly MaSuRCA MaSuRCA rackham miarka bianca snowy 2.0.3.1, 2.1.0, 2.2.1, 2.3.2, 3.1.3, 3.2.1, 3.2.2, 3.2.3, 3.3.5, 3.4.2 GPL v3
Bioinformatics assembly MetAMOS MetAMOS bianca irma milou rackham snowy 1.5rc3 GPLv2 and other open source
Bioinformatics assembly Metassembler Metassembler milou 1.5 open-source
Bioinformatics assembly MHAP MHAP milou 1.6 Apache 2.0
Bioinformatics assembly Platanus-allee Platanus-allee bianca irma rackham snowy 2.0.2 GPL v3
Bioinformatics assembly quickmerge quickmerge rackham irma bianca snowy 0.3-9233726 GPL v3
Bioinformatics assembly Unicycler Unicycler bianca irma rackham snowy 0.4.8 GPL v3
Bioinformatics assembly wtdbg2 wtdbg2 rackham irma bianca snowy 2.4 GPL v3
Bioinformatics misc AdapterRemoval AdapterRemoval bianca irma milou rackham snowy 2.1.7, 2.2.2 GPL v3
Bioinformatics misc AdmixTools AdmixTools bianca irma milou rackham snowy 5.0-20170312, 5.0-20171024, 7.0.1, 20160803 Custom "as-is" open source
Bioinformatics misc ADMIXTURE ADMIXTURE bianca irma milou rackham snowy 1.3.0 Not open source
Bioinformatics misc AlienTrimmer AlienTrimmer bianca irma milou rackham snowy 0.4.0 GPL
Bioinformatics misc ANGSD ANGSD rackham irma bianca snowy 0.917, 0.917-g6522d3e, 0.921, 0.933 None
Bioinformatics misc Athlates Athlates bianca irma milou rackham snowy 20140426 Custom
Bioinformatics misc ATLAS_aDNA ATLAS_aDNA bianca irma milou rackham snowy 20170510 None
Bioinformatics misc ATSAS ATSAS bianca irma milou rackham snowy 2.8.3-1 Academic use only
Bioinformatics misc bam2fastx bam2fastx rackham irma bianca snowy 1.3.0-80dbf79 BSD 3-clause
Bioinformatics misc bambam bambam bianca irma rackham snowy 1.4 MIT
Bioinformatics misc Bamsurgeon Bamsurgeon rackham irma bianca snowy 1.3 MIT License
Bioinformatics misc bcftools bcftools bianca irma rackham snowy 1.8, 1.10 "MIT/Expat or GPL v3"
Bioinformatics misc BEETL BEETL bianca irma milou rackham snowy 1.0.2, 1.1.0 BSD 2-Clause
Bioinformatics misc bgen bgen rackham irma bianca snowy 1.1.4 Boost Software License v1.0
Bioinformatics misc BioPerl BioPerl bianca miarka rackham 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
Bioinformatics misc bonito None rackham irma bianca snowy 0.3.7-cpu, 0.3.8, 0.4.0 Oxford Nanopore Public License 1.0
Bioinformatics misc BraCeR BraCeR rackham irma bianca snowy 2019_10_03_22e49cb Apache 2.0
Bioinformatics misc cdbfasta cdbfasta bianca irma rackham snowy 1.00 "Artistic 2.0"
Bioinformatics misc cellranger-ATAC None bianca irma rackham snowy 1.2.0, 2.0.0 None
Bioinformatics misc CheckM CheckM bianca irma rackham snowy 1.0.11, 1.0.12, 1.1.3 """"""""""""GPL v3""""""""""""
Bioinformatics misc CITE-seq-Count CITE-seq-Count rackham irma bianca snowy 1.4.3 MIT
Bioinformatics misc CleaveLand4 CleaveLand4 bianca irma milou rackham snowy 4.3 GPL v3
Bioinformatics misc CNV-seq CNV-seq milou 20140812 Misc open source
Bioinformatics misc CNVnator CNVnator bianca irma milou rackham snowy 0.3.2, 0.3.3 Creative Commons Public License
Bioinformatics misc CONCOCT CONCOCT rackham irma bianca snowy 0.4.0, 0.4.0~, 0.5.0, 1.1.0 FreeBSD
Bioinformatics misc Corset Corset bianca irma milou rackham snowy 1.04, 1.07 GPL v3
Bioinformatics misc DATES DATES rackham irma bianca snowy 753 None
Bioinformatics misc DosageConvertor DosageConvertor rackham irma bianca snowy 1.0.4 custom
Bioinformatics misc DWGSIM DWGSIM bianca irma milou rackham snowy 0.1.11-6e9a361 GPL v2
Bioinformatics misc EnsEMBL-API EnsEMBL-API rackham irma bianca snowy 87, 94 Apache License 2.0
Bioinformatics misc EPACTS EPACTS bianca miarka milou rackham snowy 3.2.6, 3.2.6_milou, 3.3.0-a5209db GPL v3
Bioinformatics misc ExpansionHunter None bianca irma rackham snowy 2.5.3, 2.5.5 None
Bioinformatics misc FastANI FastANI rackham irma bianca snowy 1.2 Apache 2.0
Bioinformatics misc fastp fastp rackham irma bianca snowy 0.20.0, 0.23.1 MIT
Bioinformatics misc fcGENE fcGENE rackham irma bianca snowy 1.0.7 GPL
Bioinformatics misc Filtlong Filtlong rackham irma bianca snowy 0.2.0 GPL v3
Bioinformatics misc FLASH FLASH bianca irma milou rackham snowy 1.2.11 GPL
Bioinformatics misc FusionCatcher None rackham irma bianca snowy 1.00, 1.10, 1.33 GPLv3
Bioinformatics misc GEM GEM bianca irma rackham snowy 2.7, 3.4 """""""""""Research only"""""""""""
Bioinformatics misc GEMMA GEMMA rackham irma bianca snowy 0.98.1 GPL3
Bioinformatics misc GeneMark GeneMark rackham miarka 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 Custom
Bioinformatics misc Genepop Genepop rackham irma bianca snowy 4.7 CeCILL (GPL compatible)
Bioinformatics misc GenomeTools GenomeTools rackham irma bianca snowy 1.5.8, 1.5.9, 1.6.1 ISC
Bioinformatics misc GERP++ GERP++ bianca irma milou rackham snowy 20110522 GPL v3+
Bioinformatics misc GTOOL GTOOL milou 0.7.5 """""""""""As is" open source""""""""""
Bioinformatics misc HiCUP HiCUP rackham irma bianca snowy 0.7.2 GPL v3 or later
Bioinformatics misc htslib htslib bianca irma rackham snowy 1.8, 1.10 "MIT/Expat and modified 3-clause BSD"
Bioinformatics misc IGV None bianca irma rackham snowy 2.3.17, 2.3.40, 2.3.92, 2.4.2, 2.8.13 None
Bioinformatics misc IGVtools IGVtools bianca irma milou rackham snowy 2.3.17, 2.3.40, 2.3.91, 2.3.98 LGPL
Bioinformatics misc IM IM bianca irma milou rackham snowy 20091217 None
Bioinformatics misc IMa2p IMa2p milou 2015-08-09 GPL v3
Bioinformatics misc IMPUTE2 IMPUTE2 bianca irma milou rackham snowy 2.3.2 """""""""""As is" open source""""""""""
Bioinformatics misc ITSx None None 1.0.9, 1.0.11, 1.1-beta, .itsx None
Bioinformatics misc KAT KAT bianca irma rackham snowy 2.0.4, 2.0.6, 2.0.8, 2.1.1, 2.3.4, 2.4.2, 2.4.2_py3.5.0, 2.4.2_py3.7.2 GPL v3
Bioinformatics misc KmerGenie None None 1.6741, 1.7039, .kmergenie None
Bioinformatics misc Kraken None rackham irma bianca miarka snowy 0.10.5-beta, 1.0, 1.1-352e780, 1.1.1, 1.1.1-20210927-375654f GPL v3
Bioinformatics misc Kraken2 Kraken2 bianca irma rackham snowy 2.0.8-beta MIT
Bioinformatics misc Krona Krona bianca miarka milou rackham snowy 2.7 Custom open source
Bioinformatics misc LASER LASER bianca irma rackham snowy 2.01, 2.02, 2.04 GPL v3
Bioinformatics misc LatentStrainAnalysis LatentStrainAnalysis milou 20160322 MIT
Bioinformatics misc LDhelmet LDhelmet bianca irma rackham snowy 1.7, 1.9, 1.10 GPL v3
Bioinformatics misc LTR_Finder LTR_Finder bianca irma rackham snowy 1.0.5, 1.0.7 Free for non-commercial use
Bioinformatics misc LUMPY LUMPY rackham irma bianca snowy 0.2.12, 0.2.13, 0.2.13-97cf18c, 0.2.13-213a417, 0.3.0 MIT
Bioinformatics misc MACE MACE milou 1.2 None
Bioinformatics misc MACS MACS bianca miarka rackham snowy 2.1.0, 2.1.2, 2.2.6, 3.0.0a6 """""BSD 3-clause"""""
Bioinformatics misc MAGeCK MAGeCK rackham irma bianca snowy 0.5.6, 0.5.9.4 BSD 3-clause
Bioinformatics misc medaka medaka rackham irma bianca snowy 0.7.1 MPL 2.0
Bioinformatics misc Meerkat Meerkat milou 0.189 Misc non-commercial open source
Bioinformatics misc MetaBat MetaBat bianca irma milou rackham snowy 0.26.3, 2.12.1 BSD-like
Bioinformatics misc METAL METAL rackham miarka bianca snowy 2011-03-25 open source
Bioinformatics misc MetaSV MetaSV bianca irma milou rackham snowy 0.5.4 BSD 2-clause
Bioinformatics misc Metaxa2 Metaxa2 rackham irma bianca snowy 2.1.3, 2.2 GPL v3
Bioinformatics misc MethPipe MethPipe rackham irma bianca snowy 3.4.3, 4.1.1 GPL v3+
Bioinformatics misc MethylDackel MethylDackel rackham irma bianca snowy 0.2.1, 0.5.1 MIT
Bioinformatics misc Mothur Mothur bianca miarka rackham snowy 1.40.5, 1.41.0 GPL v3
Bioinformatics misc ms ms rackham irma bianca snowy 20071014 open source
Bioinformatics misc MultiQC MultiQC bianca irma rackham snowy 0.6, 0.7, 0.8, 1.8, 1.9, 1.10 MIT
Bioinformatics misc NanoComp NanoComp bianca irma rackham snowy 1.9.2 GPL v3
Bioinformatics misc NanoPlot NanoPlot rackham irma bianca snowy 1.33.1 GPL3 license
Bioinformatics misc NPStat NPStat rackham irma bianca snowy 1 GPL v3 license
Bioinformatics misc nseg nseg rackham irma bianca snowy 1.0.1 Public Domain
Bioinformatics misc ont_fast5_api ont_fast5_api rackham irma bianca snowy 3.1.6 Mozilla Public License 2.0
Bioinformatics misc PCAngsd PCAngsd bianca miarka rackham snowy 0.982 """"""GPL v3""""""
Bioinformatics misc PennCNV PennCNV milou 20151014 Public domain
Bioinformatics misc phantompeakqualtools phantompeakqualtools bianca miarka milou rackham snowy 1.1 MIT
Bioinformatics misc phaser phaser rackham irma bianca snowy 20210423-5d4926d GNU
Bioinformatics misc piper piper bianca miarka rackham snowy 1.5.1 MIT
Bioinformatics misc pizzly pizzly rackham irma bianca snowy 0.37.3 BSD 2-clause
Bioinformatics misc plink2 plink2 rackham irma bianca snowy 2.00-alpha-2-20180704, 2.00-alpha-2-20190429, 2.00-alpha-2.3-20200124 GPL v3
Bioinformatics misc Porechop Porechop rackham irma bianca snowy 0.2.4 GPL v3
Bioinformatics misc prodigal prodigal bianca irma milou rackham snowy 2.6.3 GPL v3
Bioinformatics misc PRSice PRSice rackham irma bianca snowy 2.2.11.b GPL3
Bioinformatics misc psmc psmc rackham irma bianca snowy 0.6.5-r67-e5f7df5 MIT
Bioinformatics misc RECON RECON rackham irma bianca snowy 1.08 GPL
Bioinformatics misc RegScan RegScan rackham irma bianca snowy 0.5 None
Bioinformatics misc RepeatScout RepeatScout rackham irma bianca snowy 1.0.5, 1.0.6 open source
Bioinformatics misc schmutzi schmutzi rackham irma bianca snowy 20160424, 20200706-597c6bc GPL v3
Bioinformatics misc SeqAn None bianca irma rackham snowy 1.4.2, 2.4.0 None
Bioinformatics misc SeqKit SeqKit rackham irma bianca snowy 0.15.0 MIT license
Bioinformatics misc seqmonk seqmonk bianca irma milou rackham snowy 0.21.0, 0.27.0, 0.32.1, 0.34.1, 1.36.0, 1.37.1 GPL
Bioinformatics misc SMC++ SMC++ rackham irma bianca snowy 1.15.2 GPL v3
Bioinformatics misc snippy snippy rackham miarka bianca snowy 4.0, 4.0.5, 4.6.0 GPL v2 license
Bioinformatics misc spaceranger spaceranger bianca irma rackham snowy 1.0.0, 1.2.0 other
Bioinformatics misc SweeD SweeD rackham irma bianca snowy 4.0.0 GPL v3 license
Bioinformatics misc tabix tabix bianca miarka rackham snowy 0.2.6 MIT/Expat and modified 3-clause BSD
Bioinformatics misc Tombo Tombo rackham irma bianca snowy 1.5.1 Mozilla Public License 2.0
Bioinformatics misc vawk vawk rackham irma bianca snowy 0.0.1 None
Bioinformatics misc velocyto velocyto rackham irma bianca snowy 0.17.17 BSD 2-clause
Bioinformatics phylogeny CONSEL CONSEL bianca irma milou rackham snowy 0.20 None
Bioinformatics phylogeny ExaBayes ExaBayes bianca irma rackham snowy 1.5, 1.5-mpi GPL v3
Bioinformatics phylogeny FastML FastML bianca irma rackham snowy 3.1, 3.11 """"""""""""GPL v2+""""""""""""
Bioinformatics phylogeny FastTree FastTree bianca irma milou rackham snowy 2.1.8, 2.1.10 Open source "as is"
Bioinformatics phylogeny HyPhy HyPhy rackham irma bianca snowy 2.5.0, 2.5.0-mpi Custom open-source "as is"
Bioinformatics phylogeny MEGAN None None 4.70.4, 5.1.5, 5.11.3, 6.3.5, 6.10.5, 6.20.17, .MEGAN None
Bioinformatics phylogeny raxml None None 7.0.4, 7.2.7, 7.2.8, 7.3.0, 7.4.7, 8.0.20, 8.0.20-mpi, 8.2.0-gcc, 8.2.0-gcc-mpi, 8.2.0-icc, 8.2.0-icc-mpi, 8.2.0_gcc, 8.2.0_icc, 8.2.4-gcc, 8.2.4-gcc-mpi, 8.2.10-gcc, 8.2.10-gcc-mpi, 8.2.12-gcc, 8.2.12-gcc-mpi, .raxml None
Bioinformatics phylogeny RAxML-NG RAxML-NG bianca irma rackham snowy 0.9.0-mpi GNU Affero GPL v3.0
Bioinformatics pipelines fermikit fermikit bianca irma milou rackham snowy 0.14-prerelease-96f7820, r178 None
Bioinformatics pipelines nf-core nf-core rackham irma bianca snowy 1.12.1, 1.14, 2.1 MIT License
Bioinformatics pipelines nf-core-pipelines nf-core-pipelines rackham irma bianca snowy latest MIT License
Bioinformatics sw collections 454-dataanalysis 454-dataanalysis bianca irma milou rackham snowy 2.3, 2.5.3, 2.6, 2.9 None
Bioinformatics sw collections 454-dataprocessing 454-dataprocessing bianca irma milou rackham snowy 2.3 None
Bioinformatics sw collections ART ART rackham irma bianca snowy 2016-06-05 None
Bioinformatics sw collections BEDOPS BEDOPS rackham irma bianca snowy 2.4.3, 2.4.28, 2.4.39 GPL v2
Bioinformatics sw collections BEDTools BEDTools rackham irma bianca snowy 2.21.0, 2.23.0, 2.25.0, 2.26.0, 2.27.1, 2.29.2 MIT
Bioinformatics sw collections BioScope BioScope bianca irma rackham snowy 1.3.1 Commercial
Bioinformatics sw collections CASAVA CASAVA bianca miarka milou rackham snowy 1.7.0, 1.8.2 None
Bioinformatics sw collections cellranger None bianca irma rackham snowy 1.1.0, 1.3.0, 2.0.2, 2.2.0, 3.0.1, 4.0.0, 5.0.1, 6.0.2 None
Bioinformatics sw collections cellranger-ARC cellranger-ARC bianca irma rackham snowy 1.0.0 other
Bioinformatics sw collections cellranger-DNA cellranger-DNA bianca irma rackham snowy 1.1.0 other
Bioinformatics sw collections GATK GATK bianca irma milou rackham snowy 3.5.0, 3.6, 3.7, 3.8-0, 4.1.0.0, 4.1.1.0, 4.beta.5, build-20160727 BSD Style
Bioinformatics sw collections GATK-Queue GATK-Queue bianca irma milou rackham snowy 3.2.2, 3.6, 3.7, 3.8-0 MIT + academic non-commercial
Bioinformatics sw collections GenomeSTRiP GenomeSTRiP bianca irma milou rackham snowy 2.00.1650, 2.00.1685, 2.00.1710 Custom "as is" redistributable
Bioinformatics sw collections HiSeq HiSeq bianca irma milou rackham snowy 0.9 None
Bioinformatics sw collections longranger longranger bianca irma rackham snowy 2.0.1, 2.1.1, 2.1.2, 2.1.4, 2.2.2 other
Bioinformatics sw collections MEMEsuite MEMEsuite bianca irma rackham snowy 5.0.1 BSD Style
Bioinformatics sw collections supernova None bianca irma rackham snowy 1.0.0, 1.1.1, 1.1.4, 2.0.0, 2.1.1 None
Chemistry/physics ABINIT ABINIT bianca irma rackham snowy 8.10.3 GPL v3
Chemistry/physics ALPS ALPS rackham irma bianca snowy 2.3.0 ALPS Library License version 1.0, ALPS Application License version 1.0
Chemistry/physics DOCK DOCK bianca irma milou rackham 3.7 Free Academic License
Chemistry/physics gromacs None None 4.5.5, 4.5.5_intel, 4.5.7.th, 4.6.3, 4.6.3_rackham, 4.6.5, 4.6.5.th, 4.6.5_rackham, 4.6.7.th, 4.6.7.th.dp, 5.0.4, 5.0.4_rackham, 5.0.7, 5.1.1, 5.1.1_rackham, 5.1.5, 2016.1, 2016.6, 2018.6, 2018.6.th, 2019.1, 2019.1.th, 2019.6.th, 2020-GPU, 2021.1.th, .4.6 None
Chemistry/physics molcas molcas milou 7.8.082, 8.0.15-03-08 user group license
Chemistry/physics molden molden rackham 5.1 None
Chemistry/physics TmoleX TmoleX bianca irma milou rackham 18 proprietary group license
Compilers and build tools ant ant bianca irma rackham snowy 1.9.8, 1.10.0 Apache 2.0
Compilers and build tools autoconf autoconf bianca irma milou rackham snowy 2.68, 2.69 GPL
Compilers and build tools automake automake bianca irma rackham snowy 1.14.1, 1.16.1 GPL
Compilers and build tools binutils binutils rackham bianca miarka snowy 2.26, 2.28, 2.38, 2.39, 2.41 GPL v3
Compilers and build tools ddt ddt bianca irma rackham snowy 3.2.1, 5.0.1, 6.0, 6.1, 7.0 Commercial
Compilers and build tools flex flex rackham irma bianca snowy 2.6.4 modified BSD
Compilers and build tools fpc fpc rackham irma bianca snowy 3.0.4 GPL and LGPL
Compilers and build tools git git rackham bianca miarka snowy 2.5.0, 2.10.2, 2.16.1, 2.21.0, 2.24.0, 2.28.0, 2.34.1, 2.44.0 LGPL 2.1
Compilers and build tools git-lfs git-lfs rackham bianca miarka snowy 2.9.1, 3.5.1 MIT
Compilers and build tools guile guile bianca irma milou rackham snowy 1.8.8 LGPL 2.1
Compilers and build tools java java bianca bianca irma irma milou milou rackham rackham snowy snowy jdk, OpenJDK, OpenJDK_11.0.2, OpenJDK_12+32, OpenJDK_17+35, OracleJDK, OracleJDK_11.0.9, sun_jdk1.6.0_04, sun_jdk1.6.0_18, sun_jdk1.6.0_45, sun_jdk1.7.0_25, sun_jdk1.8.0_40, sun_jdk1.8.0_92, sun_jdk1.8.0_151 Other
Compilers and build tools julia julia rackham bianca miarka snowy 0.3.0-prerelease+3043, 0.3.11, 0.4.6, 1.1.1, 1.4.2, 1.6.1, 1.9.3 MIT
Compilers and build tools libtool libtool bianca irma milou rackham snowy 2.4.6 GPL
Compilers and build tools maven maven bianca irma rackham snowy 3.6.0 Apache 2.0
Compilers and build tools meson meson rackham bianca miarka snowy 0.49.2, 0.57.2, 1.1.0 None
Compilers and build tools mono mono bianca irma milou rackham snowy 3.12.0, 5.8.1.0, 5.10.1.27 Custom open source
Compilers and build tools ninja ninja rackham irma bianca snowy 1.9.0, 1.10.0 Apache 2.0
Compilers and build tools patchelf patchelf bianca miarka milou rackham snowy 0.1, 0.8 GPL v3
Compilers and build tools perl perl rackham bianca miarka snowy 5.18.2, 5.18.4, 5.22.2, 5.24.0, 5.24.1, 5.26.2, 5.32.1 GPL v1+ or Artistic License
Compilers and build tools perl6 perl6 bianca irma rackham snowy rakudo-star-2017.04, rakudo-star-2019.03 Artistic License 2.0
Compilers and build tools perl_modules perl_modules rackham bianca miarka snowy 5.18.4, 5.24.1, 5.26.2, 5.32.1 GPL v1+ or Artistic License
Compilers and build tools python None None 2.5, 2.6, 2.6.1, 2.6.5, 2.6.6, 2.7, 2.7.1, 2.7.2, 2.7.4, 2.7.6, 2.7.9, 2.7.11, 2.7.15, 2.7i, 3.1, 3.1.2, 3.1.3, 3.2, 3.2.4, 3.3, 3.3.1, 3.4.3, 3.5.0, 3.6.0, 3.6.8, 3.7.2, 3.8.7, 3.9.5, 3.10.8, 3.11.8, 3.12.1, 3.12.7, python-rpath.tcl, python-set-LD_LIBRARY_PATH.tcl, python-set-LD_LIBRARY_PATH_new.tcl None
Compilers and build tools python3 None None 3.6.0, 3.6.8, 3.7.2, 3.8.7, 3.9.5, 3.11.4, 3.11.8, 3.12.1, 3.12.7, python3-rpath.tcl None
Compilers and build tools ruby ruby bianca irma rackham snowy 2.4.1, 2.5.0, 2.6.2 Ruby license
Compilers and build tools subversion None rackham irma bianca snowy 1.9.3, 1.10.6 Apache License Version 2.0
Engineering matlab None bianca rackham snowy 7.4, 7.8, 7.10, 7.13, 8.0, 8.1, .matlab, .matlab_ny, .matlab_ny~, R2014a, R2015a, R2015b, R2016a, R2017a, R2018a, R2018b, R2019a, R2020b None
Geospatial CDO CDO rackham irma bianca snowy 1.9.5, 1.9.7.1, 1.9.7.1-intel18.3 GPL v2
Geospatial ecCodes ecCodes rackham irma bianca snowy 2.13.1 None
Geospatial FYBA FYBA bianca irma milou rackham snowy 4.1.1 Custom open-source "as is"
Geospatial GEOS GEOS rackham bianca miarka snowy 3.5.0, 3.9.1-gcc9.3.0, 3.12.0-gcc12.3.0 LGPL v2.1
Geospatial GOTM GOTM bianca irma rackham snowy 5.3-221-gac7ec88d GPL v2
Geospatial libgeotiff libgeotiff rackham bianca miarka snowy 1.4.1, 1.4.3, 1.7.1 Mixed
Geospatial Magics Magics rackham irma bianca snowy 3.3.1, 3.3.1-intel18.3 None
Geospatial NCO NCO bianca irma rackham snowy 4.8.1, 4.9.2, 4.9.3 BSD
Geospatial PROJ None snowy rackham bianca irma 6.3.2, 8.1.0 MIT
Geospatial PROJ.4 PROJ.4 bianca irma rackham snowy 4.9.2, 4.9.3, 4.9.3-intel18.3 MIT
Geospatial QGIS QGIS rackham bianca miarka snowy 3.4.12, 3.32.3 GPL license
Geospatial SHAPELIB SHAPELIB rackham irma bianca snowy 1.5.0 None
Libraries ATLAS ATLAS bianca irma milou rackham snowy 3.10.3 BSD-style
Libraries blas blas bianca irma milou rackham snowy 3.6.0 Open source
Libraries boost boost rackham bianca miarka snowy 1.41.0_gcc9.3.0, 1.44.0, 1.45.0, 1.55.0, 1.55.0_gcc4.8.3, 1.58.0-gcc8.3.0, 1.59.0_gcc4.9.2, 1.59.0_intel15.3, 1.60.0_gcc5.3.0, 1.61.0_gcc5.3.0, 1.63.0_gcc6.3.0, 1.63.0_gcc6.3.0_mpi2.0.2, 1.63.0_intel17.1, 1.66.0, 1.66.0-gcc8.3.0, 1.70.0_gcc9.1.0, 1.70.0_gcc9.1.0_mpi3.1.3, 1.70.0_gcc9.3.0, 1.70.0_gcc9.3.0_mpi3.1.5, 1.70.0_intel18.3, 1.70.0_intel18.3_intelmpi18.3, 1.70.0_intel18.3_mpi3.1.3, 1.75.0-gcc9.3.0, 1.78.0_gcc11.2.0, 1.78.0_gcc11.2.0_mpi4.1.2, 1.79.0_gcc11.2.0_mpi4.1.2, 1.81.0-gcc10.3.0, 1.83.0-gcc12.3.0, 1.83.0-gcc12.3.0-mpi4.1.5 Boost licence
Libraries bzip2 bzip2 rackham irma bianca miarka snowy 1.0.6, 1.0.8 Custom open-source "AS IS"
Libraries cairo cairo rackham irma bianca snowy 1.14.8, 1.14.12, 1.17.2, 1.17.4 LGPL v2.1 or Mozilla Public License 1.1
Libraries deal.II deal.II bianca irma rackham snowy 9.1.1-gcc, 9.1.1-intel GNU LGPL v2.1 or later
Libraries fftw fftw rackham irma bianca snowy 3.3.8 GPL
Libraries freetype freetype rackham bianca miarka snowy 2.6, 2.7.1, 2.10.1, 2.12.1 Freetype, GPL v2
Libraries giflib giflib bianca irma milou rackham snowy 5.1.4 Custom "as is"
Libraries glpk glpk bianca irma rackham snowy 4.63, 4.65 GPL
Libraries gsl gsl rackham bianca miarka snowy 1.16, 2.1, 2.3, 2.5, 2.6, 2.7 GPL
Libraries hdf4 hdf4 rackham irma bianca snowy 4.2.11_gcc4.9.2, 4.2.14-gcc6.3.0 None
Libraries hdf5 hdf5 rackham bianca miarka snowy 1.8.16_gcc4.9.2, 1.8.16_gcc5.3.0, 1.8.18, 1.8.18_gcc6.3.0, 1.10.1, 1.10.5, 1.10.5-threadsafe-intel18.3, 1.10.9, 1.14.0 HDF5 License
Libraries jemalloc jemalloc rackham bianca miarka snowy 3.6.0, 5.0.1, 5.3.0 Custom open-source
Libraries libcurl libcurl rackham bianca miarka snowy 7.45.0, 8.4.0 None
Libraries libharu libharu bianca irma milou rackham snowy 2.3.0 ZLIB/LIBPNG License
Libraries libwebp libwebp rackham bianca miarka snowy 1.0.3, 1.2.0, 1.3.0 BSD 3-clause
Libraries lpsolve lpsolve rackham irma bianca snowy 5.5.2.9 LGPL v2
Libraries netcdf netcdf bianca irma rackham snowy 4.7.1, 4.7.1-intel18.3 Custom open source "as is"
Libraries NLopt NLopt rackham irma bianca snowy 2.6.1 MIT
Libraries openblas openblas rackham bianca miarka snowy 0.2.14a, 0.2.19, 0.2.19-singlethread, 0.2.20, 0.2.20-openmp, 0.2.20-singlethread, 0.3.21, 0.3.26 BSD 3-clause
Libraries pcre pcre bianca irma milou rackham snowy 8.40 BSD 3-clause
Libraries PLplot PLplot rackham irma bianca snowy 5.15.0, 5.15.0-old_wxWidgets LGPL v2
Libraries Poppler Poppler rackham bianca miarka snowy 0.43.0, 0.54.0, 0.75.0, 23.02.0, 23.09.0 GPL v2
Libraries protobuf protobuf rackham bianca miarka snowy 3.11.4, 24.3-gcc12.3.0 Google open-source AS IS
Libraries pslib pslib rackham irma bianca snowy 0.4.6 GPL and LGPL
Libraries slurm-drmaa slurm-drmaa rackham bianca miarka snowy 1.1.2-slurm19.05.8, 1.1.4-slurm23.02.5 GPL-3.0
Libraries sparsehash None rackham irma bianca miarka snowy 2.0.2, 2.0.3, 2.0.4 BSD 3-clause
Libraries szip None milou snowy 2.1.1, 2.1_gcc4.9.2, 2.1_gcc5.3.0 None
Libraries tbb tbb milou 4.4u1_gcc4.9.2, 4.4u1_intel15.3 GPL v2
Libraries UDUNITS UDUNITS bianca irma rackham snowy 2.2.26 Custom open source "as is"
Libraries wxWidgets wxWidgets rackham irma bianca snowy 3.1.3-gtk2, 3.1.3-gtk3, 3.1.3-qt5 wxWindows Library Licence 3.1, https://github.com/wxWidgets/wxWidgets/blob/master/docs/licence.txt
Libraries Yeppp Yeppp bianca irma milou rackham snowy 1.0.0 Custom open source "as is"
Libraries zlib zlib rackham bianca miarka snowy 1.2.8, 1.2.11, 1.2.13, 1.3 None
Misc ABSOLUTE ABSOLUTE rackham bianca miarka snowy 2023-6c98496 BSD 3
Misc AdapterRemoval AdapterRemoval rackham bianca miarka snowy 2.3.1, 2.3.4 GPLv3
Misc AGAT AGAT rackham bianca miarka snowy 1.0.0, 1.3.2 GPL v3
Misc alleleCount alleleCount rackham bianca miarka snowy 4.2.1 AGPL v3
Misc ANGSD ANGSD rackham bianca miarka snowy 0.700, 0.902, 0.915, 0.940-stable GPL v2
Misc any2fasta any2fasta rackham bianca miarka snowy 0.4.2 GPL v3.0
Misc Arlequin Arlequin rackham irma bianca miarka snowy 3.5.2.2 None
Misc ARPIP ARPIP rackham bianca miarka snowy 2023.10.02-ee32c10 None
Misc bamtools bamtools rackham bianca miarka snowy 2.5.2 MIT
Misc bamUtil bamUtil rackham bianca miarka snowy 1.0.15 GPL v3
Misc bcftools bcftools rackham bianca miarka snowy 1.2, 1.19 None
Misc Beagle Beagle rackham bianca miarka snowy 4.1 GPL v3
Misc bgen bgen rackham bianca miarka snowy 1.1.6 Boost Software License v1.0
Misc BioBakery BioBakery rackham bianca miarka snowy 3.0, 3.1, 3.8 MIT license
Misc BioKIT BioKIT rackham irma bianca miarka snowy 0.0.9 Other-d
Misc BioPerl None None 1.6.1, 1.6.1_PERL5.10.1, 1.6.1_PERL5.12.3, 1.6.922, 1.6.923_Perl5.18.4, 1.7.8-perl5.32.1, .BioPerl None
Misc BUSCO BUSCO rackham bianca miarka snowy 4.1.4, 5.3.1, 5.5.0, 5.7.1 MIT
Misc Cellsnp-lite Cellsnp-lite rackham irma bianca miarka snowy 1.2.2 Apache License 2-0
Misc CHEUI CHEUI rackham bianca miarka snowy 20230518-c1c9ab6 GPL
Misc Chromium-cellranger-ATAC cellranger-ATAC rackham bianca miarka snowy 1.2.0, 2.0.0, 2.1.0 None
Misc Citup Citup rackham irma bianca miarka snowy 0.1.0 Other-d
Misc CRABS CRABS rackham irma bianca miarka snowy 0.1.2 MIT License-d
Misc CRISPResso CRISPResso rackham bianca miarka snowy 1.0.7, 2.3.1 None
Misc DamageProfiler DamageProfiler rackham bianca miarka snowy 1.1 GPL v3
Misc datamash datamash rackham bianca miarka snowy 1.8 None
Misc DATES DATES rackham bianca miarka snowy 4010 None
Misc dds-cli dds-cli rackham bianca miarka snowy milou transit latest Other
Misc deepTools deepTools rackham bianca miarka snowy 3.5.5 mixed open-source
Misc EAGLE EAGLE rackham bianca miarka snowy 1.1.3 GPL v3
Misc FAN-C FAN-C rackham bianca miarka snowy 0.9.26 None
Misc FastANI FastANI rackham bianca miarka snowy 1.33, 1.34 Apache-2.0
Misc fastK fastK rackham bianca miarka snowy 1.1.0 AS IS
Misc fastp fastp rackham bianca miarka snowy 0.23.4 MIT
Misc fgbio fgbio rackham bianca miarka snowy 2.2.1-0 MIT
Misc fineRADstructure fineRADstructure rackham bianca miarka snowy 0.3.1 Creative Commons 3.0
Misc FLAMES FLAMES rackham bianca miarka snowy 20221109-774e16a GPL v3
Misc FLASH FLASH rackham bianca miarka snowy 2.2.00 GPL v3
Misc freebayes freebayes rackham bianca miarka snowy 1.3.6, 1.3.8 MIT
Misc fsl fsl rackham bianca miarka snowy 6.0, 6.0.3 None
Misc gffread gffread rackham bianca miarka snowy 0.12.7 MIT
Misc GLIMPSE GLIMPSE rackham bianca miarka snowy 1.1.1, 2.0.0 MIT
Misc grenedalf grenedalf rackham bianca miarka snowy 0.3.0, 0.5.1, 0.6.0 GPL3
Misc GTDB-Tk GTDB-Tk rackham bianca miarka snowy 0.3.2, 1.5.0, 2.3.2, 2.4.0 GPLv3
Misc Guppy Guppy snowy miarka bianca 5.0.16-cpu, 5.0.16-gpu, 6.0.6-cpu, 6.0.6-gpu, 6.3.7-cpu, 6.3.7-gpu, 6.4.2-cpu, 6.4.2-gpu, 6.5.7-cpu, 6.5.7-gpu Custom
Misc halla halla rackham bianca miarka snowy 0.8.20 MIT
Misc HiCExplorer HiCExplorer rackham bianca miarka snowy 2.2-beta, 3.7.3 GPL v3
Misc htslib htslib rackham bianca miarka snowy 1.2, 1.19 None
Misc HUMAnN HUMAnN rackham bianca miarka snowy 3.6, 3.8 MIT license
Misc IGVtools IGVtools rackham bianca miarka snowy 2.8.13, 2.16.0 MIT
Misc Juicebox Juicebox rackham irma bianca miarka snowy 1.11.08 MIT License
Misc KING KING rackham bianca miarka snowy 2.3.2 None
Misc kingfisher kingfisher rackham bianca miarka snowy 0.3.0 GPL v3
Misc KMC KMC rackham bianca miarka snowy 3.2.2 GPL v3
Misc KneadData KneadData rackham bianca miarka snowy 0.12.0 MIT license
Misc Kraken2 Kraken2 rackham bianca miarka snowy 2.1.3-20231102-acc2248 MIT
Misc KrakenUniq KrakenUniq rackham bianca miarka snowy 0.6, 1.0.0, 1.0.1 GPLv3, MIT
Misc Krona Krona rackham bianca miarka snowy 2.7.1, 2.8.1-20211222-d1479b3 None
Misc ldsc ldsc rackham bianca miarka snowy 1.0.0, 1.0.1, 2.0.1 GPL v3
Misc MACS MACS rackham bianca miarka snowy 1.4.1, 1.4.2, 3.0.0b1 BSD 3-clause
Misc MAGeCK2 MAGeCK2 rackham irma bianca miarka snowy 20211209-435eacd BSD3
Misc mash mash rackham bianca miarka snowy 2.0, 2.3, 2.3-20210519-41ddc61 Custom open-source
Misc meryl meryl rackham bianca miarka snowy 1.4.1 Mixed open source
Misc METAL METAL rackham bianca miarka snowy 2020-05-05 open source
Misc MetaXcan MetaXcan rackham irma bianca miarka snowy 20210925-cfc9e36 MIT License-d
Misc metilene metilene rackham bianca miarka snowy 0.2-8 GPL v2
Misc mgatk mgatk rackham bianca miarka snowy 0.7.0 MIT
Misc Minimac4 Minimac4 rackham bianca miarka snowy 4.1.6 GPL-3.0
Misc mirdeep2 mirdeep2 rackham bianca miarka snowy 2.0.1.3-20220221-c6440e2 GPL v3
Misc miRDP2 miRDP2 rackham bianca miarka snowy 1.1.4, 1.1.5 GPL v3
Misc modkit modkit rackham bianca miarka snowy 0.2.5-rc2, 0.3.1, 0.3.3, 0.4.1 GPL v3
Misc mosdepth mosdepth rackham bianca miarka snowy 0.3.3 MIT
Misc Mothur Mothur rackham bianca miarka snowy 1.25.1, 1.30.1, 1.33.3, 1.36.1, 1.38.1, 1.48.0 None
Misc MRIcroGL MRIcroGL rackham bianca miarka snowy 1.2.20220720 BSD 2
Misc msisensor-pro msisensor-pro rackham bianca miarka snowy 1.2.0 None
Misc MultiQC MultiQC rackham bianca miarka snowy 1.22.2 MIT
Misc NCBI-datasets NCBI-datasets rackham bianca miarka snowy 15.29.0, 16.35.0 Public Domain, US Government
Misc ont_h5_validator ont_h5_validator rackham bianca miarka snowy 2.0.1 None
Misc picard picard rackham bianca miarka snowy 3.1.1 MIT
Misc Pisces Pisces rackham bianca miarka snowy 5.3.0.0 GPL 3
Misc plink2 plink2 rackham bianca miarka snowy 2.00-alpha-3.7-20221024, 2.00-alpha-5-20230923 GPL v3
Misc preseq preseq rackham bianca miarka snowy 3.2 GPL v3
Misc PROJ PROJ rackham bianca miarka snowy 9.1.1 MIT
Misc PyClone-VI PyClone-VI rackham irma bianca miarka snowy 20210623-6607ea1 GPL V3-d
Misc pyega3 pyega3 rackham bianca miarka snowy 5.1.0 None
Misc Raremetal Raremetal rackham bianca miarka snowy 4.15.1 None
Misc regenie regenie rackham bianca miarka snowy 3.4.1 MIT
Misc removethis removethis rackham irma bianca miarka snowy 1 None
Misc RepeatModeler RepeatModeler rackham bianca miarka snowy 2.0.4 None
Misc RGT RGT rackham bianca miarka snowy 1.0.2 GPL v3
Misc rtgcore rtgcore rackham bianca miarka snowy 3.12.1 Custom
Misc rtgtools rtgtools rackham bianca miarka snowy 3.12.1 BSD 2-clause
Misc samtools samtools rackham bianca miarka snowy 1.2, 1.19 None
Misc schmutzi schmutzi rackham bianca miarka snowy 1.5.7 GPL v3
Misc scikit-allel scikit-allel rackham bianca miarka snowy 1.3.5 None
Misc scvi-tools scvi-tools rackham bianca miarka snowy 1.0.4 BSD-3
Misc SeqKit SeqKit rackham bianca miarka snowy 2.4.0 MIT
Misc SeqLib SeqLib rackham bianca miarka snowy 1.2.0 Apache 2.0
Misc seqstats seqstats rackham bianca miarka snowy 20170404-e6f482f MIT
Misc SHAPEIT SHAPEIT rackham bianca miarka snowy v4.2.2, v5.1.1 None
Misc slivar slivar rackham irma bianca miarka snowy 0.2.7 MIT License-d
Misc SMC++ SMC++ rackham bianca miarka snowy 1.15.4, 1.15.5.dev12+g8bdecdf GPL v3
Misc smudgeplot smudgeplot rackham bianca miarka snowy 0.3 Apache-2.0
Misc sracat sracat rackham bianca miarka snowy 20210916-b896745 BSD 3-Clause
Misc sratools sratools rackham bianca miarka snowy 3.0.7 custom
Misc Stacks Stacks rackham bianca miarka snowy 2.66 GPL v3
Misc SVDB SVDB rackham bianca miarka snowy 2.8.1 MIT
Misc vcflib vcflib rackham bianca miarka snowy 1.0.9 MIT
Misc vcfstats vcfstats rackham bianca miarka snowy 0.4.2 Other
Misc vep vep rackham bianca miarka snowy 110.1, 111.0, 113.0 Apache-2.0
Misc XP-CLR XP-CLR rackham bianca miarka snowy 1.1.2 MIT
Misc applications agrep agrep bianca irma milou rackham snowy 3.41.5 ISC Open Source
Misc applications awscli awscli rackham bianca miarka snowy 1.11.140, 1.16.225, 1.29.52 Apache 2.0
Misc applications circos circos rackham irma bianca snowy 0.69-9 GPL
Misc applications cmake cmake rackham irma bianca snowy 3.5.1, 3.7.2, 3.13.2, 3.17.3 BSD 3-clause
Misc applications cowsay cowsay bianca irma milou rackham snowy 3.03 Artistic License
Misc applications Cromwell Cromwell rackham bianca miarka snowy 71, 86 BSD 3-Clause
Misc applications doxygen doxygen bianca irma milou rackham snowy 1.8.11 Gnu GPL 2
Misc applications emacs emacs rackham bianca miarka snowy 25.1, 25.2, 27.2, 28.2 GNU
Misc applications gawk gawk bianca irma milou rackham snowy 4.1.4 GPL v3
Misc applications gdl gdl bianca irma rackham snowy 1.0.0-rc.1 GPL v2
Misc applications GhostPDL GhostPDL rackham irma bianca snowy 9.53.3 Gnu GPL Affero v3
Misc applications gnuplot None None 4.4.3, 4.6.5, 5.0.7, 5.2.7, .gnuplot None
Misc applications Graphviz Graphviz rackham bianca miarka snowy 2.40.1, 9.0.0 Common Public License Version 1.0
Misc applications groff groff bianca irma milou rackham 1.22.3 GPL
Misc applications h5utils h5utils bianca irma milou rackham snowy 1.12.1 GPL v2+
Misc applications haskell-stack None bianca irma milou rackham snowy 1.0.4.3, 1.4.0, 1.7.1 None
Misc applications jq jq rackham miarka bianca snowy 1.6 MIT
Misc applications MariaDB MariaDB bianca irma milou rackham snowy 10.2.11 GPL v2
Misc applications mbuffer mbuffer bianca irma milou rackham snowy 20151002 GPL v3
Misc applications mcl mcl rackham bianca miarka snowy 14-137, 22-282 GPL v3
Misc applications metaWRAP metaWRAP rackham irma bianca snowy 1.3.2 MIT
Misc applications openbabel openbabel rackham bianca miarka snowy 3.1.1-gcc9.3.0, 3.1.1-gcc12.3.0 GPL v2
Misc applications OpenBUGS OpenBUGS rackham irma bianca snowy 3.2.3 GPL v2
Misc applications p7zip p7zip bianca irma milou rackham snowy 16.02 LGPLv2
Misc applications pandoc pandoc rackham irma bianca snowy 1.16.0.2, 2.2.3.2, 2.10.1 GPL 2
Misc applications PostgreSQL PostgreSQL bianca irma milou rackham snowy 10.3 PostgreSQL Licence
Misc applications povray povray bianca irma rackham 3.7 AGPL v3
Misc applications ROOT ROOT rackham irma bianca snowy 6.04.08, 6.06.08, 6.20.04 LGPL 2.1
Misc applications SAIGE SAIGE rackham irma bianca snowy 0.42.1 GPL v3
Misc applications SCons None None 2.5.0, .scons None
Misc applications sqlite sqlite rackham bianca miarka snowy 3.8.5, 3.11.1, 3.16.2, 3.24.0, 3.34.0, 3.45.0 public domain
Misc applications swig swig rackham bianca miarka snowy 3.0.7, 3.0.12, 4.1.1 GPL with other advice
Misc applications texinfo texinfo rackham bianca miarka snowy 6.0, 6.5, 6.6, 6.8, 7.1 GPL v3+
Misc applications texlive texlive rackham bianca miarka snowy 2015, 2016, 2018, 2019, 2021, 2023-08-14, 2024-04-24 None
Misc applications tinyutils None None 1.1, 1.2, 1.3, 1.4, .tinyutils-1.1 None
Misc applications tmux tmux rackham bianca miarka snowy 2.5, 3.1b, 3.3a Custom open-source AS IS
Misc applications vim None rackham irma bianca snowy 8.0-1360, 8.1-1053, 8.2.3701 VIM License
Misc applications xz xz rackham bianca miarka snowy 5.2.2, 5.2.6, 5.4.5 Mixed open-source
Parallel gnuparallel gnuparallel rackham bianca miarka snowy 20140222, 20150522, 20170122, 20180822, 20230422 GPL v3+
Phylogeny Dsuite Dsuite rackham bianca miarka snowy 0.5-r57 open-source
Phylogeny FastME FastME rackham bianca miarka snowy 2.1.6.2, 2.1.6.4 GPL
Phylogeny FastTree FastTree rackham bianca miarka snowy 2.1.11 GPL v2+
Phylogeny G-Nomix G-Nomix rackham bianca miarka snowy 2022-09-18-de952a2 free for academic use
Phylogeny HyPhy HyPhy rackham bianca miarka snowy 2.5.51-mpi None
Phylogeny iqtree iqtree rackham bianca miarka snowy 2.2.2.6-omp-mpi GPL v2
Phylogeny KIN KIN rackham bianca miarka snowy 3.1.3, 3.1.3-20230612-76dc469 GPL v3
Phylogeny MetaPhlAn4 MetaPhlAn4 rackham bianca miarka snowy 4.0 MIT license
Phylogeny paml paml rackham bianca miarka snowy 4.10.7 other
Phylogeny pathPhynder None rackham irma bianca snowy 1.a-20221011-a407a97, 2020-12-19-b8532c0 MIT
Phylogeny phylip phylip rackham bianca miarka snowy 3.697 None
Phylogeny PhyloPhlAn PhyloPhlAn rackham bianca miarka snowy 3.0.3 MIT license
Phylogeny phyx phyx rackham bianca miarka snowy 1.3 GPL-3.0
Phylogeny read2tree read2tree rackham bianca miarka snowy 0.1.5-20240117-ff2d167 MIT
Phylogeny snphylo snphylo rackham bianca miarka snowy 20180901 None
Pipelines 3D-DNA 3D-DNA rackham irma bianca miarka snowy 20190801-529ccf4 MIT License
Pipelines biomodal biomodal rackham bianca miarka snowy 1.0.2 commercial
Pipelines cactus_atac cactus_atac rackham bianca miarka snowy 1.0.0 MIT
Pipelines cutadapt cutadapt rackham bianca miarka snowy 4.5, 4.8 MIT
Pipelines GenoPredPipe GenoPredPipe rackham bianca miarka snowy 20211104-02777ce, 20221121-e3caf6b GNU GPL v3
Pipelines happy happy rackham bianca miarka snowy 1.0.0 MIT
Pipelines Juicer Juicer rackham bianca miarka snowy 1.6, 2.0 MIT License
Pipelines Juicer_tools Juicer_tools rackham irma bianca miarka snowy 1.6, 1.22.01 MIT License
Pipelines MPRASuite MPRASuite rackham bianca miarka snowy 1.0.3 MIT
Pipelines nextNEOpi nextNEOpi rackham bianca miarka snowy 1.4.0 https://github.com/icbi-lab/nextNEOpi/blob/master/LICENSE
Pipelines nf-core nf-core rackham bianca miarka snowy 2.4.1, 2.6, latest MIT License
Pipelines Panaroo Panaroo rackham bianca miarka snowy 1.2.10, 1.3.2 MIT
Pipelines ParseBiosciences-Pipeline ParseBiosciences-Pipeline rackham bianca miarka snowy 1.4.0 Custom
Pipelines qiime2 qiime2 rackham bianca miarka snowy 2024.1, 2024.2 BSD 3-Clause
Pipelines SALSA SALSA rackham irma bianca miarka snowy 20220408-ed76685 MIT License
Pipelines Seurat Seurat rackham bianca miarka snowy 5.0.2, 5.1.0 MIT
Pipelines SMRT SMRT rackham bianca miarka snowy 13.0.0.207600 None
Pipelines snakemake snakemake rackham bianca miarka snowy 5.32.2, 8.20.1 MIT License
Pipelines star-fusion star-fusion rackham bianca miarka snowy 1.9.1, 1.10.1 BSD 3-clause
Pipelines ViWrap ViWrap rackham bianca miarka snowy 1.3.0 GPL v3
Statistics nonmem None rackham irma bianca snowy 7.3.0, 7.4.3, 7.4.4, 7.5.0 Commercial
Statistics PsN PsN rackham irma bianca snowy 5.0.0 GPL 2+
Statistics R None None 2.8, 2.8.1, 2.10, 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, 3.0.1, 3.0.2, 3.1.0, 3.2.2, 3.2.3, 3.3.0, 3.3.1, 3.3.2, 3.3.2_rackham, 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, 4.2.1, 4.3.1, 4.3.2, 4.4.1, .R, R.tcl None
Statistics R_packages R_packages rackham bianca miarka snowy 3.3.0, 3.3.1, 3.3.2, 3.4.0, 3.4.3, 3.5.0, 3.5.2, 3.6.0, 3.6.1, 4.0.0, 4.0.4, 4.1.1, 4.3.1 Various
Statistics RStudio RStudio rackham bianca miarka snowy 1.0.136, 1.0.143, 1.0.153, 1.1.423, 1.1.463, 1.4.1106, 2022.02.0-443, 2022.02.3-492, 2022.07.1-554, 2023.06.0-421, 2023.06.2-561, 2023.12.1-402, 2024.04.2-764 Custom
Sw_collections bbmap bbmap rackham bianca miarka snowy 39.06, 39.08 Public Domain
Sw_collections BEDOPS BEDOPS rackham bianca miarka snowy 2.4.41 GPL v2
Sw_collections BEDTools BEDTools rackham bianca miarka snowy 2.20.1, 2.31.1 MIT
Sw_collections cellbender cellbender rackham bianca miarka snowy 0.3.0 BSD-3
Sw_collections Chromium-cellranger cellranger rackham bianca miarka snowy 4.0.0, 5.0.1, 6.0.2, 6.1.2, 7.0.0, 7.0.1, 7.1.0, 8.0.1 None
Sw_collections Chromium-cellranger-ARC cellranger-ARC rackham bianca miarka snowy 1.0.0, 2.0.2 https://support.10xgenomics.com/docs/license
Sw_collections DRAGEN DRAGEN rackham bianca miarka snowy 4.1.5 None
Sw_collections GATK GATK rackham bianca miarka snowy 1.0.4105, 1.0.5365, 1.0.5909, 1.2.12, 1.4.5, 1.4.21, 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, 3.4-46, 3.4.0, 3.4.46, 4.0.8.0, 4.1.4.1, 4.3.0.0 None
Sw_collections MEMEsuite MEMEsuite rackham bianca miarka snowy 4.11.1, 4.11.2_1, 5.1.1, 5.5.1 University of California open-source AS IS
Sw_collections SpeedPPI SpeedPPI rackham bianca miarka snowy 2023.07.11-37d0a03 None
Uncategorized alphafold alphafold rackham bianca miarka snowy 2.3.1 None
Uncategorized alphafold_dataset alphafold_dataset rackham bianca miarka snowy 2.0.0, 2.1.1, 2.3.1 None
Uncategorized Amber None snowy 16-GPU, 18-GPU None
Uncategorized amber_previous None None amber.tcl, ambertools18_intel_python2 None
Uncategorized AmpliconNoise None bianca miarka rackham snowy 1.27 None
Uncategorized AnnotSV None bianca irma rackham snowy 1.1.1 None
Uncategorized annovar_data None bianca miarka rackham snowy 2019.10.21, 2021.05.18 None
Uncategorized Ansys Ansys rackham bianca miarka snowy 19.1, 19.5, 2020R1, 2023R2 commercial software
Uncategorized apr None rackham irma bianca snowy 1.7.0 Apache License 2.0
Uncategorized apr-util None rackham irma bianca snowy 1.6.1 Apache License Version 2.0
Uncategorized archspec archspec rackham bianca miarka snowy 0.2.4 Apache 2.0, MIT
Uncategorized aria2 aria2 rackham bianca miarka snowy 1.36 OpenSSL
Uncategorized Armadillo None rackham irma bianca snowy 7.900.0, 9.700.2 Apache License V2.0
Uncategorized ascp ascp rackham bianca miarka snowy 4.2.0.183804, 4.4.3.891 None
Uncategorized athena None bianca miarka rackham snowy 1.1 None
Uncategorized BackSPIN None rackham irma bianca snowy 20171211_2fbcf5d BSD 2-Clause
Uncategorized BAM-matcher None None 20160611, .bammatcher, .bammatcher~ None
Uncategorized Bandage None milou 0.8.0 None
Uncategorized bazel bazel rackham bianca miarka snowy 7.0.0-pre.20230917.3 None
Uncategorized bcftools-MoCha None rackham irma bianca snowy 1.9-20191129, 1.11-20210315, 2019-11-29 None
Uncategorized BclConverter None bianca irma milou rackham snowy 1.7.1 None
Uncategorized BioBakery_data BioBakery_data rackham bianca miarka snowy 3.0-20210423, 3.1-20231102 None
Uncategorized BisSNP None None 0.82.2, .bissnp None
Uncategorized BLAKE2 BLAKE2 rackham bianca miarka snowy 20230212-ed1974e CC0-1.0 or OpenSSL or Apache Public Licence 2.0
Uncategorized Bracken None rackham irma bianca snowy 2.5 GPL v3
Uncategorized bubblewrap bubblewrap rackham irma bianca miarka snowy 0.6.2 LGPL v2+
Uncategorized BUSCO_data BUSCO_data rackham bianca miarka snowy latest None
Uncategorized CAMMiQ None rackham irma bianca miarka snowy 20211015-6142150 MIT License
Uncategorized CAP3 None milou 08-06-13, .CAP3, CAP3 None
Uncategorized capnproto capnproto rackham bianca miarka snowy 1.0.2 MIT
Uncategorized CAT None rackham irma bianca snowy 20190926-e25443 Apache License 2.0
Uncategorized cellranger-ARC-data None bianca irma rackham snowy 2020-A None
Uncategorized cellranger-ATAC-data None bianca irma rackham snowy 1.2.0, 2.0.0 None
Uncategorized cellranger-data cellranger-data rackham bianca miarka snowy 1.1.0, 1.2.0, 3.0.0, 2020-A, 2024-A None
Uncategorized cellranger-DNA-data None bianca irma rackham snowy 1.0.0 None
Uncategorized cellranger-VDJ-data cellranger-VDJ-data rackham bianca miarka snowy 4.0.0, 5.0.0, 7.1.0 None
Uncategorized chain_files chain_files rackham bianca miarka snowy 20230825 Open access
Uncategorized ChEMBL ChEMBL rackham bianca miarka snowy 22.1, 33 Creative Commons Attribution-ShareAlike 3.0 Unported license
Uncategorized ChimeraSlayer None bianca miarka rackham snowy 20110519 None
Uncategorized Chromium-cellranger-DNA None rackham irma bianca snowy 1.1.0 https://support.10xgenomics.com/docs/license
Uncategorized Chromium-longranger None rackham irma bianca snowy 2.2.2 Misc non-commercial
Uncategorized Chromium-spaceranger None rackham irma bianca snowy 1.0.0 None
Uncategorized circlator None rackham irma bianca snowy 1.5.5 GNU General Public License v3.0
Uncategorized clapack clapack rackham bianca miarka snowy 3.2.1 Public domain
Uncategorized clearcut None bianca irma rackham snowy 1.0.9 None
Uncategorized ClonalFrameML None bianca irma milou rackham snowy 1.11-4f13f23 None
Uncategorized conda None rackham irma bianca snowy latest © Copyright 2017, Anaconda, Inc. Revision 6be5194b.
Uncategorized coreutils None bianca irma milou rackham snowy 8.25, 8.27 None
Uncategorized CPLEXOptimizationStudio None rackham irma bianca miarka snowy 12.9.0, 20.1 IBM Academic
Uncategorized CROP None rackham irma bianca miarka snowy 1.33 Other-d
Uncategorized CS-Rosetta None rackham irma bianca snowy 1.01_Rosetta_3.7 None
Uncategorized CST_Studio CST_Studio rackham bianca miarka snowy 2023.0 None
Uncategorized CTAT_RESOURCE_LIB None bianca miarka rackham snowy 2017-11, 2018-02, 2019-08 None
Uncategorized cuda cuda rackham bianca miarka snowy 11.2.1, 11.7.0, 11.8.0, 12.0.0, 12.1.0, 12.1.1, 12.2.0, 12.2.2 EULA
Uncategorized cuDNN cuDNN rackham bianca miarka snowy 8.1.0.77, 8.4.1.50, 8.6.0.163, 8.7.0.84, 8.8.0.121, 8.9.2.26 SLA
Uncategorized CUT-RUNTools None rackham irma bianca miarka snowy 2 MIT
Uncategorized cyrus-sasl None rackham irma bianca snowy 2.1.27 None
Uncategorized darsync darsync rackham bianca miarka snowy 20240208-7ff09d9 None
Uncategorized dbCAN dbCAN rackham bianca miarka snowy 11 None
Uncategorized DBdeployer DBdeployer rackham irma bianca miarka snowy latest Apache-2
Uncategorized ddt-perf None milou rackham 7.0 None
Uncategorized desmond desmond rackham irma bianca miarka snowy 2022-2 gpl
Uncategorized Dfam Dfam rackham bianca miarka snowy 3.7, 3.8 Creative Commons Zero CC0
Uncategorized Dfam-TE-Tools None rackham irma bianca snowy 1.4 CC0 1.0 Universal
Uncategorized DFTB+ None rackham snowy 19.1 GNU LGPL-3
Uncategorized dlib None bianca irma rackham snowy 19.15 None
Uncategorized dssp None None 2.0.4 None
Uncategorized edlib edlib rackham bianca miarka snowy 1.2.7 MIT
Uncategorized Eigen None bianca irma rackham snowy 3.3.4 None
Uncategorized eLSA None bianca irma milou rackham 20160907-febe2d7a57c8 None
Uncategorized ESPResSo None rackham 4.1.4 GPLv3
Uncategorized estout None rackham irma bianca snowy 20200417-d392e71 MIT license
Uncategorized fastq_screen_data fastq_screen_data rackham bianca miarka snowy 20220330 None
Uncategorized freesurfer freesurfer rackham bianca miarka snowy 6.0.0, 7.4.1 Custom open-source
Uncategorized funannotate_data funannotate_data rackham bianca miarka snowy 1.8.17 BSD-2
Uncategorized GAAS None rackham irma bianca miarka snowy 1.2.0 GPL v3
Uncategorized gamess None bianca irma rackham 20070324R1, 20070324R1-kalkyl, 20101001R1-kalkyl-intel-12.1-mvapich2, 20110818R1-kalkyl-intel12.0-mvapich2, 20170930 None
Uncategorized gaussian None milou rackham snowy .g09, .gaussian, .gv, .gv~, g03, g03.d02, g03.e01, g09, g09.a02, g09.c01, g09.d01 None
Uncategorized gaussview None None 5.0.8, .gv, .gv~ None
Uncategorized gcc None None 4.2.3, 4.3.0, 4.3.2, 4.3.2-test, 4.3.2t, 4.4, 4.4.2, 4.4.3, 4.4.4, 4.5.0, 4.6.2, gcc, gcc4.3, gcc4.4, gcc4.5, gcc4.6.tcl None
Uncategorized gdb None rackham irma bianca miarka snowy 11.2 Other-d
Uncategorized gdc None None 2.064.2_4.8, .gdc None
Uncategorized genomescope None rackham irma bianca snowy 1.0.0_d2aefdd Apache-2.0
Uncategorized genomescope2.0 None rackham irma bianca snowy 1.0.0_5034ed4 Apache-2.0
Uncategorized GetOrganelleDB GetOrganelleDB rackham bianca miarka snowy 0.0.1, 0.0.2 GPLv3
Uncategorized glib glib rackham irma bianca miarka snowy 2.72.1 LGPL 2.1+
Uncategorized GlimmerHMM None rackham irma bianca snowy 3.0.4 Open Source, licence file in cluded
Uncategorized GMP GMP rackham bianca miarka snowy 6.3.0 LGPL v3; GPL v2
Uncategorized go go rackham bianca miarka snowy 1.11.5, 1.20.3 Go licence
Uncategorized GoogleCloudSDK GoogleCloudSDK rackham bianca miarka snowy 447.0.0, 455.0.0 None
Uncategorized grocsvs None rackham irma bianca snowy 0.2.5 MIT
Uncategorized gromacs-plumed None rackham 2019.4.th None
Uncategorized gromacs-saxs None rackham 2020.04-9edbdbc None
Uncategorized gstreamer None milou 0.10.31 None
Uncategorized GTDB GTDB rackham bianca miarka snowy R04-RS89, R202, R214.1, R220 None
Uncategorized Gurobi Gurobi rackham bianca miarka snowy 9.5.1, 10.0.2, 11.0.3 Academic License
Uncategorized gzip gzip rackham bianca miarka snowy 1.12, 1.13 GPL v3
Uncategorized HG002_Q100_T2T_assembly HG002_Q100_T2T_assembly rackham bianca miarka snowy 0.7 CC0
Uncategorized HHsuite None None 2.0.16, 2.0.16~ None
Uncategorized HLA-LA None rackham irma bianca snowy 1.0.1-20201001-f636b62 None
Uncategorized hyperqueue hyperqueue rackham 0.18.0 MIT license
Uncategorized iGenomes None rackham irma bianca snowy latest None
Uncategorized ImageJ ImageJ rackham bianca miarka snowy 1.52j, 1.54g None
Uncategorized IMAP None rackham irma bianca snowy 1.0 None
Uncategorized Immcantation None rackham irma bianca snowy 4.0.0 AGPL-3
Uncategorized imputor None bianca miarka rackham snowy 20180829 None
Uncategorized InterOp None bianca miarka rackham snowy 1.1.4 None
Uncategorized jamovi jamovi rackham bianca miarka snowy 2.3.21 Mixed
Uncategorized jansson None rackham irma bianca snowy 2.12 MIT
Uncategorized JasPer None bianca irma rackham snowy 2.0.14 None
Uncategorized JsonCpp JsonCpp rackham bianca miarka snowy 1.9.5 Dual Public Domain/MIT
Uncategorized kermit None rackham irma bianca snowy 1.0 MIT
Uncategorized Kraken_data None bianca irma rackham snowy latest None
Uncategorized KrakenUniq_data KrakenUniq_data rackham irma bianca miarka snowy latest GPLv3, MIT
Uncategorized KyotoTycoon None bianca irma rackham snowy stable-20170410 None
Uncategorized Label-Studio Label-Studio rackham bianca miarka snowy 1.10.1dev Apache-2.0
Uncategorized lammps None rackham 29Oct2020_gcc_openmpi, 30Jul2016_intel_mkl, 31Mar2017_gcc_openmpi None
Uncategorized libarchive libarchive rackham bianca miarka snowy 3.6.2 New BSD
Uncategorized libb2 libb2 rackham bianca miarka snowy 0.98.1 CC0-1.0
Uncategorized libdeflate libdeflate rackham bianca miarka snowy 1.19 MIT
Uncategorized libicu None rackham irma bianca miarka snowy 5.2-4 MIT and UCD and public domain
Uncategorized liblzma None milou 5.2.2 None
Uncategorized librdf librdf rackham bianca miarka snowy 1.0.17 LGPL 2.1, GPL 2, Apache 2
Uncategorized librsvg None rackham irma bianca snowy 2.48.4 LGPL 2.1
Uncategorized libSBML libSBML rackham bianca miarka snowy 5.20.2 LGPL v2.1
Uncategorized libtiff libtiff rackham bianca miarka snowy 4.5.0 A IS
Uncategorized libvips libvips rackham bianca miarka snowy 8.15.2 LGPL-2.1
Uncategorized lighter None bianca irma rackham snowy 1.1.1 None
Uncategorized LLVM None rackham irma bianca miarka snowy 13.0.1 Various
Uncategorized LoFreq None None 2.1.2, .lofreq None
Uncategorized longranger-data None bianca irma rackham snowy 2.0.0, 2.1.0 None
Uncategorized LRSDAY None rackham irma bianca snowy 1.5.0 MIT
Uncategorized LTR_retriever None rackham irma bianca snowy 2.9.0 GPL v3
Uncategorized lz4 None rackham irma bianca snowy 1.9.2 BSD 2-Clause & GPLv2
Uncategorized lzo None rackham irma bianca snowy 2.1 GPL v2+
Uncategorized m4 None bianca irma milou rackham snowy 1.4.17 None
Uncategorized mathematica None rackham snowy 11.2 None
Uncategorized mauve None bianca miarka milou rackham snowy 2015-02-13 None
Uncategorized mesos None rackham irma bianca snowy 1.9.0 Apache-2.0
Uncategorized metaMATE None rackham irma bianca miarka snowy 20220327-3cdacd7 Other-d
Uncategorized metaSNV None rackham irma bianca miarka snowy 1.0.3, 2.0.1 misc free software
Uncategorized miniconda2 None irma rackham snowy 4.5.4 None
Uncategorized miniconda3 None irma rackham snowy 4.5.4 None
Uncategorized miniforge miniforge rackham bianca miarka snowy latest None
Uncategorized mlst None bianca miarka rackham snowy 2.12 None
Uncategorized MMseqs2_data MMseqs2_data rackham bianca miarka snowy 20230125, 20230816, 20240202 None
Uncategorized Moses Moses rackham bianca miarka snowy 4.0 LGPL v2.1
Uncategorized mp-tools mp-tools rackham bianca miarka snowy latest None
Uncategorized MPFR MPFR rackham bianca miarka snowy 4.2.1 LGPL v3+
Uncategorized mpjexpress None milou .mpjexpress, v0.38 None
Uncategorized MultiBUGS None rackham miarka bianca snowy 2.0 LGPL v3.0
Uncategorized MUMPS MUMPS rackham 5.5.0, 5.5.0-hybrid CeCILL-C license
Uncategorized nanopolish None rackham irma bianca snowy 0.12.0 MIT
Uncategorized ncbi_taxonomy None rackham irma bianca miarka snowy latest None
Uncategorized ncftp None bianca irma rackham snowy 3.2.6 None
Uncategorized ncview None rackham snowy 2.1.7, 2.1.7-intel-2019b GPL 3 license
Uncategorized ngsF-HMM None milou 20160614 None
Uncategorized NINJA None rackham irma bianca snowy 0.97-cluster_only MIT
Uncategorized NMRPipe None rackham irma bianca snowy 10.4 https://www.ibbr.umd.edu/nmrpipe/terms.html
Uncategorized nullarbor None bianca miarka rackham snowy 2.0.20180819 None
Uncategorized octave None bianca irma rackham snowy 5.1.0 None
Uncategorized opam opam rackham irma bianca miarka snowy 2.1.2 LGPL 2.1 with special modifications
Uncategorized OpenFOAM None rackham irma bianca snowy 6, 7, v1912 GNU GPLv3
Uncategorized OpenJPEG OpenJPEG rackham bianca miarka snowy 2.3.0, 2.5.0 BSD 2-clause
Uncategorized ORCA None None 4.0.1.2, 4.2.1, 5.0.4, 6.0.0, 6.0.1, .4.0.1.2 None
Uncategorized panther panther rackham bianca miarka snowy 14.1, 15.0, 17.0, 18.0 Custom
Uncategorized paraview None None 5.6, 5.9.1, .paraview_noQT, .paraview_noQT~ None
Uncategorized PCAP None milou PCAP None
Uncategorized pcre2 pcre2 rackham bianca miarka snowy 10.42 PCRE2 Licence
Uncategorized PGAP None rackham irma bianca miarka snowy 2022-02-10.build5872 Mixed
Uncategorized PHP PHP rackham bianca miarka snowy 7.4.32 PHP License v.3.0.1
Uncategorized PhylogicNDT None rackham irma bianca miarka snowy 2020 None
Uncategorized phylophlan None bianca irma milou rackham snowy 0.99 None
Uncategorized pigz pigz rackham bianca miarka snowy 2.4, 2.8 Custom AS IS
Uncategorized plumed None rackham irma bianca snowy 2.6.0, 2.7.1-gcc LGPL-3.0
Uncategorized pm-tools pm-tools rackham bianca miarka snowy latest None
Uncategorized python_GIS_packages python_GIS_packages rackham bianca miarka snowy 3.10.8 Various
Uncategorized python_ML_packages python_ML_packages snowy 3.9.5-cpu, 3.9.5-gpu, 3.11.8-cpu, 3.11.8-gpu Various
Uncategorized PyTorch PyTorch rackham bianca miarka snowy 1.12.0-cpu BSD-modified
Uncategorized qctool None rackham bianca irma snowy 2-5559450, 2-beta None
Uncategorized QoRTs None rackham irma bianca snowy 1.3.6 MIT
Uncategorized QuantumESPRESSO None rackham 6.7MaX-Release GNU GPLv2
Uncategorized rawcopy None rackham irma bianca snowy 1.1 None
Uncategorized RDKit RDKit rackham irma bianca miarka snowy 20220301 BSD 3-Clause-d
Uncategorized readline None rackham irma bianca miarka snowy 6.2-11 GPL v3
Uncategorized rfmix None bianca irma rackham snowy v2 None
Uncategorized Rosetta None rackham irma bianca snowy 3.7, 2019.4 https://els.comotion.uw.edu/licenses/86
Uncategorized RSPt None rackham 2019-08-30, 2020-06-10 GPL2 license
Uncategorized rspt None None 1951_intel_mkl, 2003_intel_mkl, 2018-03-31_intel_mkl, rspt.tcl None
Uncategorized rust rust rackham bianca miarka snowy 1.43.1, 1.67.0, 1.77.0 Apache 2.0\, MIT
Uncategorized sbcl None None 1.0.12, .sbcl None
Uncategorized scikit-learn None rackham irma bianca snowy 0.22.1 BSD 3
Uncategorized sda-cli sda-cli rackham bianca miarka snowy 0.1.0, 0.1.3 AGPL-3.0
Uncategorized SDSL None rackham irma bianca miarka snowy 2.1.1 GPLv3
Uncategorized Siesta None rackham irma bianca snowy 4.1-b4, 4.1-MaX-1.0 GNU GPLv3
Uncategorized siesta None None 3.2-pl4_intel_mkl, 4.1-b3_intel_mkl, siesta-2018.tcl, siesta.tcl None
Uncategorized silva None bianca irma rackham snowy 128, 132, 138.1 None
Uncategorized simpleitk None rackham irma bianca snowy 1.2.4 Apache 2.0
Uncategorized Singular None rackham irma bianca snowy 4.1.2 GNU GPL
Uncategorized smoove None rackham irma bianca snowy 0.2.5 Apache 2.0
Uncategorized snp-sites None bianca irma rackham snowy 2.4.0 None
Uncategorized snpEff_data snpEff_data rackham bianca miarka snowy 5.1, 5.2 MIT
Uncategorized SourceTracker None bianca miarka rackham snowy 0.9.5 None
Uncategorized spaceranger-data None bianca irma rackham snowy 1.0.0, 2020-A None
Uncategorized spm None bianca irma rackham 12 None
Uncategorized SPRKKR None rackham snowy 7.7.1, 7.7.3 GPL license
Uncategorized SQuIRE None rackham irma bianca miarka snowy 0.9.9.9a-beta, 885bf4d-20190301 GPL v3
Uncategorized SRPRISM None rackham irma bianca miarka snowy 3.2.7 Public domain
Uncategorized SuiteSparse SuiteSparse rackham bianca miarka snowy 5.8.1, 7.7.0 Multiple
Uncategorized sumaclust None bianca irma rackham snowy 1.0.00 None
Uncategorized sunstudio None None 12.1, 12.1u1, .sunstudio None
Uncategorized SvABA None rackham irma bianca snowy 1.1.3-20201112-0f60e36 GPL v3
Uncategorized svviz None rackham irma bianca snowy 1.6.4 MIT
Uncategorized swarm None bianca irma rackham snowy 1.2.19 None
Uncategorized SymEngine None rackham irma bianca snowy 0.7.0 MIT
Uncategorized tapestri None rackham irma bianca snowy 2.0.1 None
Uncategorized tcl None bianca irma rackham snowy 8.6.8 None
Uncategorized TelomereHunter None bianca irma rackham snowy 1.0.4 None
Uncategorized tesseract None rackham irma bianca snowy 4.1.3 Apache-2.0
Uncategorized TEtranscripts None rackham irma bianca snowy 2.2.1 GPL3
Uncategorized totalview None None 8.8.0-2, 8.9.2-0, 8.9.2-2, 8.10.0-1, 8.15.0-15, totalview None
Uncategorized turbo None None 6.00, 6.01, 6.1, 6.02, .turbo None
Uncategorized turbomole None bianca irma milou rackham 7.3 None
Uncategorized umap None bianca irma rackham snowy 0.3.7 None
Uncategorized utf8proc None rackham irma bianca snowy 2.5.0 MIT
Uncategorized Vampire Vampire rackham snowy 6.0 GPL
Uncategorized vasp None None 4.6.34_intel_mkl, 4.6_intel_mkl, 5.2.8_intel_mkl, 5.2.11_intel_mkl, 5.2.12_intel_mkl, 5.2_intel_mkl, 5.3.3_intel_mkl, 5.4.1_intel_mkl, 5.4.1_openmpi_intelmkl, 5.4.4_intel_mkl, .vasp_acml, vasp, vasp.save, vasp.tcl, vasp.tcl_2013, vasp.tcl_2014, vasp.tcl_2017, vasp.tcl_2017_intelmpi, vasp.tcl_2017_openmpi, vasp_new None
Uncategorized vasp_acml None None 4.6.28, 4.6.34, 4.6.36, .vasp_acml None
Uncategorized vasp_goto None None 4.6.28, 4.6.34, 4.6.36, .vasp_goto None
Uncategorized VMD VMD rackham bianca miarka snowy 1.9.4-alpha-57 University of Illinois Open Source License
Uncategorized VSCodium VSCodium rackham bianca miarka snowy latest MIT
Uncategorized vtk None None 6.1.0, .vtk None
Uncategorized Whisper Whisper rackham bianca miarka snowy 0.5.1, 20240930 None
Uncategorized Whisper-gui Whisper-gui rackham bianca miarka snowy 0.1, 0.2, 0.3 None
Uncategorized WhisperX WhisperX rackham bianca miarka snowy 3.1.1 None
Uncategorized wine wine rackham bianca miarka snowy 7.0 None
Uncategorized WPS None rackham snowy 4.1 None
Uncategorized WPS-geog None rackham snowy 4 Custom open-source AS IS
Uncategorized WRF None bianca irma rackham snowy 4.1.3, 4.1.3-dmpar None
Uncategorized WRFg None rackham snowy 3.8.1 Custom AS-IS
Uncategorized XCrySDen None rackham irma bianca snowy 1.5.60, 1.6.2 GNU GPLv2
Uncategorized zig zig rackham bianca miarka snowy 0.9.1, 0.11.0 MIT
Uncategorized zsh None bianca irma rackham snowy 5.7.1 None
Uncategorized zstd zstd rackham irma bianca miarka snowy 1.5.2 GPL v2