Difference between revisions of "Installed Software"
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| Line 1,553: | Line 1,553: | ||
| [[Trimmomatic]] || 0.32, 0.33, 0.36 || [http://www.usadellab.org/cms/index.php?page=trimmomatic] || Biology, NGS | | [[Trimmomatic]] || 0.32, 0.33, 0.36 || [http://www.usadellab.org/cms/index.php?page=trimmomatic] || Biology, NGS | ||
|- | |- | ||
| − | | [[Trinity]] || | + | | [[Trinity]] || r20161120-2.3.2, r20170205-2.4.0 || [http://trinityrnaseq.sourceforge.net/] || Biology, NGS, RNA-Seq |
|- | |- | ||
| [[Trinotate]] || 2.0.1, 3.0.1 || [http://trinotate.github.io/] || Biology | | [[Trinotate]] || 2.0.1, 3.0.1 || [http://trinotate.github.io/] || Biology | ||
Revision as of 13:47, 21 July 2017
- Last updated on 2017-07-21.bes
- Up to three latest versions are listed. The default is shown in bold if it's not the latest version.
- See output of 'module spider module_name' for a full list of provided versions.
A B C D E F G H I J K L M N O P Q R S T U V W X Y
| Name | Version [1] | Website | Category |
|---|---|---|---|
| 3PCLR | 20150906 | [1] | Biology, Genomics |
| 4P | 1.0 | [2] | Biology, SNP |
| AbInit | 6.12.3, 7.10.2, 7.10.4 | [3] | Quantum Chemistry, DFT |
| Abyss | 1.5.2, 1.9.0, 2.0.0 | [4] | Biology, NGS |
| ADMB | 11.5 | [5] | Math, Modeling, Optimization |
| AdmixTools | 20150311, 20160513 | [6] | Biology, Bioinformatics, Genomics, NGS |
| ADMIXTURE | 1.23, 1.3.0 | [7] | Biology, Bioinformatics, Genomics, NGS |
| AEGeAn | 0.14.0 | [8] | Biology, Genomics |
| AFNI | 2013_11_24, 2016_0_19 | [9] | Biology, Statistics, Imaging, Neurology |
| Agalma | 0.2.1, 0.3.5, 0.5.0 | [10] | Biology, Bioinformatics, Genomics, SNP |
| AGOUTI | 0.3.3 | [11] | Biology, Genomics |
| ALE | 20150507 | [12] | Biology, Bioinformatics, Assembly |
| AltAnalyze | 1.9.6 | [13] | Biology, Genomics |
| ALLPATHS-LG | 42316, 44837 | [14] | Biology, NGS |
| Amber | 11, 12, 14, 16 | [15] | Simulation, chemistry |
| AMAS | 0.98 | [16] | Biology, Sequence Alignment |
| AMOS | 3.1.0 | [17] | Biology, Genomics, NGS |
| AMPHORA2 | 20140305 | [18] | Biology, Phylogenetics |
| AMPtk | 0.8.0, 0.8.5 | [19] | Biology, Bioinformatics, NGS |
| ANGEL | 2.3 | [20] | Biology, Bioinformatics, NGS |
| Anvio | 2.0.2, 2.1.0, 2.3.2 | [21] | Biology, Microbial 'omics |
| ANNOVAR | 20120621, 20150322 | [22] | Biology, Genomics |
| AStalavista | 3.2 | [23] | Biology, NGS, RNA-Seq, Genomics |
| ASTRID | 20150807 | [24] | Biology, Genomics |
| ASPECT | 1.5.0 | [25] | Simulation, Geology |
| Atlas | 3.10.1, 3.11.17 | [26] | Library, Math |
| Amuse | 6.0, 10.0 | [27] | Astrophysics |
| ANGSD | 20150306, 20150909 | [28] | Biology, NGS |
| Affymetrix Power Tools | 1.15.0, 1.18.0 | [29] | Biology, Genomics, Microarray |
| ArrayFire | 3.4.2 | [30] | Code Optimization |
| ARC | 20140312 | [31] | Biology, NGS |
| ARCS | 1.0.0, 1.0.1 | [32] | Biology, Genomics |
| Armadillo | 6.200.3 | [33] | Library, C++ , Math |
| Astral | 4.10.6, 4.10.7, 5.0.3 | [34] | Biology, Bioinformatics, NGS, Phylogenetics |
| AtomEye | 3 | [35] | Material Science |
| ATRAM | 20140624 | [36] | Biology, NGS |
| Augustus | 2.6, 3.2.1, 3.2.2 | [37] | Biology, NGS |
| Auto3DEM | 4.05.1, 4.05.2 | [38] | Image Reconstruction |
| BamBam | 1.0 | [39] | Biology, NGS |
| BALI-PHY | 2.3.8 | [40] | Bioinformatics, Bayesian Estimation |
| BAMM | 2.5.0 | [41] | Biology, Phylogenetics |
| Bam-readcount | 20150216 | [42] | Biology, NGS |
| Bamstats | 20140602 | [43] | Biology, NGS |
| Bamtools | 2.1.1 | [44] | Biology, NGS |
| BamUtil | 1.0.2 | [45] | Biology, NGS |
| Bam-Readcount | 20150616 | [46]] | Biology, Genomics |
| BAPS | 6.0 | [47] | Biology, Populaton genetics |
| Barrnap | 0.7 | [48] | Biology, RNA-Seq |
| Basemount | 0.1.2.464 | [49] | Biology, DNA Sequencing |
| BatVI | 1.00 | [50] | Biology, Phylogenetics |
| BayArea | 1.0.2 | [51] | Biology |
| BayeScan | 2.1 | [52] | Biology, SNP |
| BayesR | 20151016 | [53] | Biology, Phylogenetics |
| BayeScEnv | 1.1 | [54]] | Biology, SNP, Phylogenetics |
| BayesRate | 1.3.43 | [55] | Biology, Phylogenetics |
| Bbcp | 12.08.17.00.0 | [56] | Network file transfer |
| BBMap | 36.23, 37.09 | [57] | Biology, Alignment |
| Bcbio-nextgen | 0.8.7, 0.9.9 | [58] | Biology, NGS |
| Bcftools | 1.2, 1.3.1, 1.4 | [59] | Biology, Genomics, NGS |
| Bcl2fastq | 2.16 | [60] | Biology, NGS, Illumina |
| BEAGLE | 3.2.2, 4.0 | [61] | Biology, Genetics, Genotyping |
| BEAST | 1.7.5, 1.8.1, 2.3.2 | [62] | Biology, Phylogenetics |
| Bedops | 2.4.2 | [63] | Biology, Bioinformatics, Sequence, NGS |
| BEDTools | 2.23.0, 2.24.0, 2.26.0 | [64] | Biology, NGS |
| BEST | 2.3.1 | [65] | Biology, Phylogenetics |
| BESST | 2.2.4 | [66] | Biology, Bioinformatics |
| BETA | 1.0.5 | [67] | Biology, NGS |
| BFAST | 0.7.0 | [68] | Biology, NGS |
| Bismark | 0.7.7, 0.13.0, 0.17.0 | [69] | Biology, NGS, Methylation |
| BinPacker | 1.0 | [70] | Biology, RNA-Seq, Sequence Assembly |
| BinSanity | 0.1.3, 0.2.5.9 | [71] | Biology, Genomics |
| Bioconductor | Latest | [72] | Biology, R, Statistics |
| BioPerl | 1.006901 | [73] | Biology, Perl |
| BioPython | 1.59 | [74] | Biology, Python |
| BLASR | 20130815 | [75] | Biology, NGS |
| NCBI BLAST | 2.2.27, 2.5.0, 2.6.0 | [76] | Biology, Sequence alignment |
| Blast2go | 2.5.0-20120705 | [77] | Biology, Annotation |
| BLAT | 20120524, 20140318 | [78] | Biology, Sequence alignment |
| Blender | 2.63 | [79] | Graphics |
| BLESS | 1.02 | [80] | Biology, NGS |
| BLUPF90 | 20160604 | [81] | Biology, Phylogenetics |
| BoltzTraP | 1.2.5 | [82] | Physics |
| Boost | 1.49.0, 1.59.0, 1.63.0 | [83] | C++, Library |
| Bowtie | 0.12.9, 1.1.1, 1.2.0 | [84] | Biology, NGS |
| Bowtie2 | 2.2.9, 2.3.0, 2.3.2 | [85] | Biology, NGS |
| BPP | 1.9.0, 2.2, 3.2 | [86] | Biology, Phylogenetics |
| Bracken | 1.0.0 | [87] | Biology, Phylogenetics |
| BRANCH | 1.8.1 | [88] | Biology, NGS, Mapping |
| BRATNextGen | 20150505 | [89] | Biology, Genomics |
| BRIG | 0.95 | [90] | Biology, Genomics |
| Bsoft | 1.9.1 | [91] | Biology, Image Analysis |
| Bsmap | 2.74, 2.87 | [92] | Biology, NGS, Methylation |
| BSSeeker2 | 2.1.0 | [93] | Biology, Phylogenetics |
| BUCKy | 1.4.4 | [94] | Biology, Genomics |
| BUSCO | 1.22, 2.0b, 3.01 | [95] | Biology, Genomics |
| Bwa | 0.6.1, 0.7.12, 0.7.15 | [96] | Biology, NGS |
| BXH_XCEDE_tools | 1.11.1 | [97] | Biology, Bioinformatics |
| Camino | 20140723 | [98] | Biology, Neuroscience, Imaging |
| Canu | 1.1, 1.3, 1.5 | [99] | Biology, Sequencing |
| CASM | 0.2.0 | [100] | Statistical Mechanics |
| CAP3 | 20120705 | [101] | Biology, Sequence Assembly |
| CASAVA | 1.8.2 | [102] | Biology, NGS |
| CD-HIT | 4.6, 4.6.4 | [103] | Biology, Genomics |
| CDO | 1.6.1, 1.7.2rc5 | [104] | Climate |
| CEAS | 1.0.2 | [105] | Biology, Genomics |
| CellProfiler | 2.0 | [106] | Biology, Image Analysis |
| CellRanger | 1.2.1, 1.3.0 | [107] | Biology, Bioinformatics, NGS, RNA-Seq |
| CFITSIO | 3.370 | [108] | Library, C |
| CGATools | 1.6.0.42 | [109] | Biology, NGS |
| Charmm | 36a3 | [110] | Simulation, Chemistry |
| Chartdirector | 5.1.0 | [111] | Graphics |
| CheckM | 1.0.4 | [112] | Biology, Genomics |
| Chimera | 1.7 | [113] | Biology, Modeling |
| ChromEvol | 2.0 | [114] | Biology, Phylogenetics |
| CIMS | 4.1.2 | [115] | Biology, Genomics |
| Circos | 0.63-pre11, 0.69-2 | [116] | Biology, Visualization |
| Circlator | 1.5.1 | [117] | Biology, Genomics |
| CIRCexplorer | 1.1.10 | [118] | Biology, Bioinformatics, RNA-Seq |
| CisGenome | 2.0 | [119] | Biology, Genomics, Peak Calling |
| Clann | 3.2.3 | [120] | Biology, Phylogenetics |
| CLARK | 1.2.2-b | [121] | Biology, Genomics |
| CLHEP | 2.2.0.1 | [122] | High Energy Physics |
| CLIPper | 1.0 | [123] | Biology, Sequencing |
| CLIPSeqTools | 0.1.7 | [124] | Biology, Sequencing |
| ClonalFrame | 1.1, 1.2 | [125] | Biology, Genomics, NGS |
| ClonalFrameML | 1.25 | [126] | Biology, Genomics, NGS |
| ClustalW | 2.1 | [127] | Biology, Genomics |
| Cluster3 | 1.52 | [128] | Biology, Genomics |
| Clview | 20130402 | [129] | Biology, Genomics |
| ClustalO | 1.2.0 | [130] | Biology, Genomics |
| CLUMPP | 1.1.2 | [131]] | Biology, Bioinformatics |
| ClusterFinder | 313 | [132] | Biology, Metabolomics |
| CMake | 2.8.8, 2.9.12.1, 3.1.0 | [133] | Programming, Build System |
| CMS | 20170518 | [134] | Biology |
| CMWP | 140518 | [135] | Biology, Genomics |
| CNVnator | 0.3.2 | [136] | Biology, Genomics |
| CNVSeq | 20110715 | [137] | Biology, NGS |
| Cobrapy | 0.3.2 | [138] | Biology, Metabolomics, Modeling |
| Coevol | 1.3c, 1.4b | [139] | Biology, Phylogenetics |
| CoMap | 1.4.1 | [140] | Biology, Genomics |
| CONSEL | 0.20 | [141] | Biology, Phylogenetcs |
| CONCOCT | 0.3.1 | [142] | Biology, Genomics |
| ContaVect | 0.2 | [143] | Biology, Phylogenetics |
| CoNIFER | 0.2.2 | [144] | Biology, Genomics |
| Consed | 23.0 | [145] | Biology, Genomics |
| Coreutils | 8.23 | [146] | GNU Utilities, Computer Science |
| Corset | 1.06 | [147] | Biology, NGS |
| covNMR | 2014 | [148] | Biochemistry |
| CPAT | 1.2.2 | [149] | Biology, Phylogenetics |
| CPLEX | 12.6.5 | [150] | Optimizer |
| CUDA | 4.2, 5.5 | [151] | Programming, Graphics |
| Crass | 1.0.1 | [152] | Biology, Assembly |
| CRISPRdigger | 1.007 | [153] | Biology, Phylogenetics |
| CrossMap | 0.2.3 | [154] | Biology, Genomics |
| Crux | 1.40 | [155] | Biology, Mass-Spectrometry |
| CryptoMiniSat | 5.0.1 | [156] | SAT |
| Cufflinks | 1.3.0, 2.0.2, 2.2.1 | [157] | Biology, NGS |
| Cutadapt | 1.7.1, 1.8.1, 1.10 | [158] | Biology, NGS |
| CUTE | 20160116, 20161010 | [159] | Cosmology |
| Cytoscape | 3.4.0 | [160]] | Biology, Bioinformatics |
| DAKOTA | 5.4.0 | [161] | Computational Science |
| DaPars | 0.9.0 | [162] | Biology, NGS, RNA-Seq |
| DALIGNER | 1.0 | [163] | Biology, Sequencing |
| Datamash | 1.1.0 | [164] | Math |
| DCMTK | 3.6.0 | [165] | Biology, Neuroscience, Imaging |
| DSSAT | 4.5 | [166] | Biology |
| dDocent | 20160425 | [167] | Biology |
| DDSCAT | 7.3.0 | [168] | Astrophysics |
| DDT | 5.0, 6.0, 6.1.2, 7.0.4 | [169] | Software |
| Dealii | 8.3.0, 8.4.1, 8.5.0 | [170] | Library |
| DeconSeq | 0.4.3 | [171] | Biology, Phylogenetics |
| Delft3D | 3621 | [172] | Hydrodynamics, Physics |
| DeepPicker | 20161102 | [173] | Deep Learning, Cross-Molecule Training |
| DeepTools | 2.4.3 | [174] | Biology, Bioinformatics, NGS |
| Desmond | 3.0.3.1 | [175] | Simulation, Biology, Chemistry |
| DETONATE | 1.9, 1.11 | [176] | Biology, NGS |
| DEXTRACTOR | 1.0 | [177] | Biology, Sequencing |
| Dalton | 2011 | [178] | Quantum Chemistry |
| Diamond | 0.5.1, 0.8.5 | [179] | Computational Biology, Genomics |
| DiscoSnp | 2.2.10 | [180] | Biology, Phylogenetics, SNP |
| Dibig Tools | 1.0 | [181] | Bioinformatics, PBS, Torque, Jobs |
| DiffReps | 1.55.4 | [182] | Biology, NGS, ChIP-Seq |
| Dindel | 1.01 | [183] | Biology, NGS |
| DISCOVARdenovo | 52488 | [184] | Biology, NGS |
| DIYABC | 1.0.4.43b, 2.0.3 | [185] | Biology, Genomics |
| Dlpoly | 4.03.4 | [186] | Simulation, Biology, Chemistry |
| Dlpoly-Classic | 1.9 | [187] | Simulation, Biology, Chemistry |
| DNA Clust | 3.0 | [188] | Biology, Genomics |
| Dock | 6.5, 6.6, 6.7 | [189] | Chemistry, ligand binding prediction |
| DOT | 2.0 | [190] | Biology, Bioinformatics, Docking |
| DosageConvertor | 1.0.3 | [191] | Biology, Converter |
| Doxygen | 1.8.3.1 | [192] | Programming, Documentation |
| DSK | 2.1.0 | [193] | Biology, NGS |
| DSSP | 2.2.1 | [194] | Biology, Molecular Dynamics |
| DTI-TK | 2.3.1 | [195] | Biology, Neurology, Imaging |
| EA-Utils | 1.1.2.537 | [196] | Biology, NGS |
| ECTools | 20140311, 20141201 | [197] | Biology, Sequencing, Bioinformatics |
| ECE | 1.0 | [198] | Ece |
| EEGLAB | 12.0.2.1b, 13.2.2b, 13.4.4b | [199] | Biology, Matlab |
| ED2 | 2.1 | [200] | Biology |
| eGene-MVN | 0.1 | [201] | Biology, Genetics |
| eigenMT | 20160228 | [202] | Biology, Genetics |
| EIGENSOFT | 4.2, 5.0.1, 6.0.1 | [203] | Biology, Population |
| emboss | 6.5.7 | [204] | Biology, multi-tool suite |
| EMAN2 | 2.11 | [205] | Biology |
| EMMAX | 20100307, 20120210 | [206] | Biology, NGS, Mapping |
| EMC | 9.3.9 | [207] | Monte Carlo Simulations |
| EMIRGE | 20130727 | [208] | Biology, NGS |
| Ensembl_Tools | 80 | [209] | Biology, Bioinformatics |
| EPACTS | 3.2.6 | [210] | Biology, Bioinformatics, Genomics |
| EPOCH | 4.7.3 | [211] | Astronomy, CPPP |
| eQTLA | 1.1 | [212] | Biology, Genomics |
| Eqtlbma | 1.2.2 | [213] | Biology, Genotyping |
| Esmf | 6.3.0rp1 | [214] | Climate |
| Espresso | 5.0.1, 5.2.0, 5.2.1, 5.3.0 | [215] | Modeling, Physics |
| ESPRIT | 201211 | [216] | Biology, NGS, Metagenomics |
| ETE2 | 2.1 | [217] | Biology, Phylogenetics |
| ETE3 | 3.0.0 | [218] | Biology, Phylogenetics |
| Eval | 2.2.8 | [219] | Biology, Genomics, GUI |
| ExaBayes | 1.4.1, 1.5 | [220] | Biology, Phylogenetics |
| ExaML | 1.0.5, 1.0.12, 3.0.14, 3.0.17 | [221] | Biology, Phylogenetics |
| ExomeCNV | 1.4 | [222] | Biology, NGS, Genomics |
| Exonerate | 2.2.0 | [223] | Biology, Genomics |
| eXpress | 1.3.1 | [224] | Biology, NGS |
| FALCON | 20160828, 20161222 | [225] | Biology, Bioinformatics, NGS, Sequencing |
| FALCON_unzip | 20160623, 20161222 | [226] | Biology, Bioinformatics |
| FAR | 2.15 | [227] | Biology, Genomics |
| FASTA | 34.26.5, 36.3.6d | [228] | Biology, Genomics |
| FAST-iCLIP | 0.9.1 | [229] | Biology, Sequencing |
| FastML | 3.0 | [230] | Biology, Phylogenetics, ML |
| FastSpar | 0.0.4 | [231] | Biology, Genomics |
| FastQC | 0.10.1, 0.11.2, 0.11.4 | [232] | Biology, NGS |
| Fastq-tools | 0.7, 0.8 | [233] | Biology, NGS |
| FastStructure | 20150112 | [234] | Biology, Genomics |
| FastTree | 2.1.7 | [235] | Biology, Phylogenetics |
| Fastx_toolkit | 0.0.13.2 | [236] | Biology, NGS |
| Fathmm | 20150225 | [237] | Biology, Genomics |
| fcGENE | 1.0.7 | [238] | Biology, Genomics, SNP |
| Ferret | 6.82 | [239] | Oceanography, Meteorology |
| FFmpeg | 2.1.3, 2.8.3 | [240] | Multimedia, audio, video |
| FFTW | 3.3.2, 3.3.3, 3.3.4 | [241] | Math, Library, C++ |
| FineSTRUCTURE | 2.0.7 | [242] | Biology, Populatiopn Genetics |
| FLASH | 1.2.10, 1.2.11 | [243] | Biology, Genomics, NGS |
| Flexbar | 2.3 | [244] | Biology, Genomics, NGS |
| Fluent | 14.5.7, 15.0.7, 16.0, 17.2 | [245] | Simulation, Fluid Dynamics |
| fqtools | 20160224 | [246] | Biology, Bioinformatics, NGS |
| FragGeneScan | 1.16 | [247] | Biology, NGS, Genomics |
| FrameDP | 1.2.2 | [248] | Biology, Sequencing |
| Frealign | 9.11 | [249] | Image Reconsctruction |
| FreeBayes | 1.0.1, 1.0.2, 1.1.0 | [250] | Biology, NGS, SNP Calling |
| FREEC | 9.6 | [251] | Biology, Sequencing |
| Freesurfer | 5.2.0, 5.3.0 | [252] | Biology, Neurology, Imaging |
| FSL | 5.0.2.2 | [253] | Biology, Neurology, Imaging |
| Galaxy | latest | [254] | Biology, Chemistry, Other |
| GapFiller | 1.11 | [255] | Biology, NGS |
| Garli | 2.0, 2.01 | [256] | Biology, Phylogenetics |
| GAML | 20150610 | [257] | Biology, NGS |
| GAMBIT | 15.1.0, 16.0.0 | [258] | Game Theory |
| GARM | 0.7.4 | [259] | Biology, NGS |
| GASVPro | 201310 | [260] | Biology, NGS, Genomics |
| GATE | 7.0 | [261] | Data Analysis |
| GATK | 1.6.9, 3.4.46, 3.5.0 | [262] | Biology, NGS |
| Gaussian | G03, G09-A.02, G09-C.01 | [263] | Modeling, Computational Chemistry |
| Gblocks | 0.91b | [264] | Genomics, Alignment tool |
| GCTA | 1.24.7, 1.26.0 | [265] | Biology, Genomics, SNP |
| GDAL | 1.11.2 | [266] | Geospatial Data Modeling, Geospatial Library |
| GDC-Client | 1.0.1 | [267] | Biology, Bioinformatics, Sequencing, NGS |
| Geant4 | 4.10 | [268] | Physics |
| GEM | 20130406 | [269] | Biology, NGS |
| gem5 | 2.0 | [270]] | Computer Simulator |
| GEMINI | 4.6.6a, 0.13.1, 0.18.0 | [271] | Biology, Genomics, Genetics |
| GenBank Tools | 20140130 | [272] | Biology, Genomics |
| GeneMark | 2012.04 | [273] | Biology, Genomics, Metagenomics |
| GeneSeqer | 20140226 | [274] | Biology, Genomics |
| Genewise | 2.2.0 | [275] | Biology, Genomics, Annotation |
| GenGen | 1.0.1 | [276] | Biology, Phylogenetics |
| Genome STRiP | 2.00.1602 | [277] | Biology, genomics, NGS |
| GenomicConsensus | 20160523 | [278] | Biology, Phylogenetics |
| GenomicTools | 2.7.0 | [279] | Biology, NGS |
| GenomeTools | 1.5.7 | [280] | Biology, Bioinformatics |
| GenotypeHarmonizer | 1.4.18 | [281] | Biology, Bioinformatics |
| GenSel | 4.90 | [282] | Biology, Genetics |
| GET_HOMOLOGUES | 20150529 | [283] | Biology, Genomics |
| GFOLD | 1.1.4 | [284] | Biology, RNA-seq |
| Gffread | 0.9.8c | [285] | Biology, Bioinformatics |
| GKNO | 1.30.18 | [286] | Biology, NGS, |
| Git | 1.8.2.1, 1.9.0 | [287] | Development, Revision Control |
| Glimmer | 3.02 | [288] | Biology, Microbial Annotation |
| Globus | 2.1.3 | [289] | Data Transfer |
| GLPK | 4.55 | [290] | Biology, Genomics |
| Gmap | 20150723, 20160501, 20160816 | [291] | Biology, Genomics |
| GNU Compilers | 5.2.0 | [292] | Compilers, Programming |
| GnuPlot | 4.6.0, 5.0.3 | [293] | Graphics, Plotting, Programming |
| Grace | 5.1.22 | [294] | Graphics, plotting, 2D |
| GrADS | 2.0.1 | [295] | Earth Science |
| GramCluster | 1.3 | [296] | Biology, Sequencing |
| GRASS | 7.0 | [297] | Geography |
| GraphViz | 2.38.0 | [298] | Graphics, plotting, visualization |
| GraphMap | 0.4.0 | [299] | Biology, Sequencing |
| Gromacs | 4.5.5, 4.6.5, 5.1.2 | [300] | Chemistry, Modeling, Simulation |
| GSNP | 1.0 | [301] | Biology, Bioinformatics, NGS |
| GSL | 1.15 | [302] | Library, Math, C++, C |
| Gsutil | 4.15 | [303] | Cloud, Storage, Google |
| Gubbins | 20150519, 20160421 | [304] | Biology, Phylogenetics, Genomics |
| GULP | 4.0 | [305] | Material Science |
| HaMStR | 13.2.2, 13.2.3, 13.2.4 | [306] | Biology, Genomics |
| HapCompass | 0.7.7 | [307] | Biology, NGS, Genomics |
| HAPCUT | 0.7 | [308] | Biology, Assembly |
| Hapsembler | 2.21 | [309] | Biology, Genomics, NGS |
| HapTree | 1.0 | [310] | Biology, Genomics, NGS |
| hapQTL | 1.00 | [311] | Biology, Genomics |
| HDF4 | 4.2.11 | [312] | Library, Data |
| HDF5 | 1.8.9, 1.8.15, 1.10.1 | [313] | Library, Data |
| HGTFinder | 20160720 | [314] | Biology, Genomics |
| HISAT2 | 2.0.0b, 2.0.1b, 2.0.3b | [315] | Biology, Sequence Alignment, NGS |
| HMMER3 | 3.0, 3.1b1, 3.1b2 | [316] | Biology, Genomics |
| HMMSplicer | 0.9.5 | [317] | Biology, Genomics |
| HOMER | 4.2, 4.7, 4.8 | [318] | Biology, Genomics |
| HOOMD | 1.3.3 | [319] | Chemistry |
| HTMLDoc | 1.2.82 | [320] | Documentation, PDF, HTML |
| HTSeq | 0.5.3p3, 0.6.1p1 | [321] | Biology, NGS |
| Hyb | 20141126 | [322] | Biology, NGS, RNA-Seq |
| HybPiper | 1.2 | [323] | Biology, Phylogenetics |
| HyPhy | 2.1.2.28, 2.2.6.1 | [324] | Biology, Phylogenetics |
| Hypre | 1.10.0b, 2.8.0b | [325] | Library, Math, Physics |
| iAssembler | 1.32 | [326] | Biology, Assembly |
| IBDNe | 20150815 | [327] | Biology, NGS |
| iCommands | 3.3.1 | [328] | Biology, iPlant, Data Tansfer |
| ICORN2 | 0.95 | [329] | Biology, Sequencing |
| IDBA-UD | 1.0.9, 1.1.0, 1.1.1 | [330] | Biology, NGS |
| IDBA-MT | 1.0 | [331] | Biology, NGS |
| IEP | 3.6 | [332] | Programming, Python, Editor |
| IGB | 8.4.1 | [333] | Biology, Genomics, NGS |
| IGV | 2.3.91 | [334] | Biology, Bioinformatics, NGS |
| iGTP | 1.1 | [335] | Biology, Bioinformatics, Phylogenetics |
| illumiprocessor | 20150803 | [336] | Biology, Sequencing |
| IM and IMa | 20091217 | [337] | Biology, Population |
| IMa2 | 20120827 | [338] | Biology, Population |
| ImageJ | 1.48 | [339] | Image manipulation |
| ImageMagick | 6.8.8-9, 7.0.5-5 | [340] | Image manipulation |
| IMOD | 4.7.15 | [341] | 3D modeling, Image Reconstruction |
| InParanoid | 4.1 | [342] | Biology, Bioinformatics |
| Intel Compilers | 2016.0.109 | [343] | Programming, Compilers |
| IOAPI | 3.1 | [344] | Meteorology |
| Interproscan | 4.8 | [345] | Biology, Genomics, Iprscan, Interproscan |
| ipyrad | 0.4.4, 0.6.20 | [346] | Biology, bioinformatics, NGS |
| IQ-TREE | 1.4.0, 1.4.2, 1.5.3 | [347] | Biology, Phylogenetics |
| IRAP | 0.8.1p7 | [348] | Biology, NGS, RNA-seq |
| iRep | 20161015 | [349] | Biology, |
| IRFinder | 1.0.0, 1.2.0 | [350] | Biology, RNA-Seq |
| ITK | 4.3.1 | [351] | Biology, Genomics |
| ITK-SNAP | 3.0.0 | [352] | Biology, Neuroscience, Imaging |
| JACUSA | 1.2.0 | [353] | Biology, NGS |
| JAGS | 3.3.0 | [354] | Statistics |
| Java | 1.7.0_79, 1.8.0_31 | [355] | Java Development Kit |
| Je | 1.0. | [356] | Biology, NGS |
| Jellyfish | 2.1.1 | [357] | Biology, NGS |
| JModelTest | 2.1.1 | [358] | Biology, Phylogenetics, Genomics |
| Julia | 0.3.11, 0.4.6 | [359] | Programming, Languages |
| KaKs | 1.2 | [360] | Biology, Phylogenetics |
| Kent | 20120524 | [361] | Biology, NGS |
| Khmer | 1.1, 2.0, 2.1 | [362] | Biology, NGS |
| KIM | 1.7.2 | [363] | Library |
| KING | 1.4, 1.9 | [364] | Biology, Genomics |
| Kinfin | 1.0.1 | [365] | Biology, Phylogenetics |
| KisSplice | 2.4.0-p1 | [366] | Biology, NGS |
| Kallisto | 0.42.3, 0.42.4 | [367] | Biology, NGS, RNA-Seq |
| KERAS | 1.0.8 | [368] | Deep Learning |
| Kmer | 1934 | [369] | Biology, NGS |
| KmerGenie | 1.6741 | [370] | Biology, NGS, Utilities |
| Kraken | 0.10.4b | [371] | Biology, Genomics, Phylogenetics |
| Krona | 20161019 | [372] | Biology, Bioinformatics |
| kSNP | 3.021 | [373] | Biology, Phylogenetics, SNP |
| Lace | 0.99 | [374] | Biology, NGS |
| LAMMPS | 28Oct12, 30Sep13, 28Jun14 | [375] | Molecular Dynamics Simulation |
| LAMP | 2.5 | [376] | Biology, Genomics |
| Last | 247, 531, 801 | [377] | Biology, Sequence alignment |
| Lastz | 1.03.02, 1.02.00 | [378] | Biology, NGS |
| LDhat | 2.2a | [379] | Biology, Genomics |
| LIBSVM | 3.12 | [380] | Machine Learning |
| LIGR | 2.05 | [381] | Biology, Assembly |
| LINKS | 1.8.5 | [382] | Biology, Genomics |
| LFMM | 1.4 | [383] | Biology, Genomics |
| LSC | 0.3, 0.3.1 | [384] | Biology, NGS, Error correction |
| lobSTR | 4.0.6 | [385] | Biology, Phylogenetics |
| Loci | 3.3 | [386] | Fluid Dynamics |
| LoRMA | 0.3 | [387] | Biology, NGS |
| LS-DYNA | 700, 711, 800 | [388] | Physics |
| LTRReteriever | 20170514 | [389] | Biology, Phyloegenetics |
| Lumpy | 0.2.1 | [390] | Biology, SNP |
| LZO | 2.09 | [391] | Library, Data Compression |
| MACH | 1.0.18 | [392] | Biology, Genomics |
| Mach2VCF | 20150515 | [393] | Biology |
| M5tools | 20121126 | [394] | Biology, Bioinformatics, Genomics |
| MACS | 1.4.2, 2.1.1 | [395] | Biology, ChIP-Seq |
| mafft | 7.215, 7.245, 7.294 | [396] | Biology, Multiple sequence alignment |
| Mash | 1.1 | [397] | Biology, Genomics |
| Maker | 2.25b, 2.31.6, 2.31.8 | [398] | Biology, Annotation, Genomics |
| MapSplice | 2.1.7 | [399] | Biology, NGS, RNA-Seq |
| MAPminer | 1.1 | [400] | Biology, Phylogenetics |
| MassMine | 0.9.5, 0.10.0, 0.11.0 | [401] | Data Mining |
| Maq | 0.7.1 | [402] | Biology, NGS |
| MARK | 2.0.1 | [403] | Statistics |
| MarkerMiner | 20150429, 20150511 | [404] | Biology, Genomics |
| MaryGold | 0.2 | [405] | Biology, NGS |
| MaSuRCA | 2.3.2, 3.2.1 | [406] | Biology, NGS |
| Matlab | 2012a, 2013a, 2014a | [407] | Math, Simulation, Programming |
| MATS | 3.0.8, 3.0.9, 3.2.5 | [408] | BIology, NGS |
| Mauve | 2.3.1 | [409] | Biology, NGS |
| MaxBin | 2.1.1 | [410] | Biology, NGS |
| MCarts | 1.0.2 | [411] | Biology, Genomics, Markov models |
| MCNP | 5, 6b2, 6, 6.1 | [412] | Physics |
| MCNPX | 2.7.0, 2.7.0-i8 | [413] | Physics |
| MEGAN | 5.10.3, 6.4.15 | [414] | Biology, NGS |
| MEGAHIT | 1.1.1 | [415] | Biology, NGS |
| Megraft | 1.0.2 | [416] | Biology, Sequencing |
| Melting | 4.3.1 | [417] | Biology, Genome, RNA, Folding |
| Meme | 4.11.1, 4.11.2 | [418] | Biology, Motifs, Sequence analysis |
| Meraculous | 2.0.5 | [419] | Biology, NGS |
| Mercurial | 4.0.2 | [420] | Development, Revision Control |
| Merlin | 1.1.2 | [421] | Biogolgy, SNP |
| Meta-Tissue | 0.4 | [422] | Biology, Genetics |
| Metabin | 1.0 | [423] | Biology, Metagenomics |
| MetaCluster | 5.0b | [424] | Biology, Metagenomics |
| MetaCV | 2.3.0 | [425] | Biology, NGS |
| METAL | 20110325 | [426] | Biology, Genomics |
| MetAMOS | 1.5.0rc4-20140827 | [427] | Biology, Bioinformatics, Genomics, Assembly |
| Metassembler | 1.5 | [428] | Biology, Genomics |
| MetaVelvet | 1.2.01 | [429] | Biology, NGS |
| Metaxa2 | 2.0.2, 2.1.1 | [430] | Biology, NGS |
| MetaGeneMark | 2012.04 | [431] | Biology, Genomics |
| Mfold | 3.6 | [432] | Biology, Genomics |
| MGEScan | 1.1 | [433] | Biology, Genomics |
| MHAP | 1.6 | [434] | Biology, Sequencing |
| MIA | 20130301 | [435] | Biology, NGS |
| MicrobeCensus | 1.0.7 | [436] | Biology, NGS |
| MIDAS | 20160830 | [437] | Biology, Phylogenetics |
| Midnight Commander | 4.6.1 | [438] | Tools, Utilities |
| Migrate-n | 3.3.0, 3.6.6, 3.6.11 | [439] | Biology, Population |
| Minced | 0.2.0 | [440] | Biology, Genomics |
| Minimac | 2-20140915, 3-20151015 | [441] | Biology, Genomics |
| Minimap | 0.2 | [442] | Biology, Phylogenetics |
| mira | 3.9.18, 4.0.rc1, 4.0.2 | [443] | Biology, NGS |
| MIReNA | 2.0 | [444] | Biology, Phylogenetics |
| MISO | 0.4.9, 0.5.2, 0.5.3 | [445] | Biology, NGS |
| MKL | 2016.0.109, 2017.1.132 | [446] | Library, Math |
| MMSEQ | 1.0.8 | [447] | Biology, NGS |
| MSMBuilder | 2.5.1 | [448] | Molecular Dynamics |
| MOABS | 1.2.9, 1.3.2, 1.3.4 | [449] | Biology, NGS, Genomics |
| Modeller | 9.11, 9.13, 9.14 | [450] | Biology, Modeling |
| Molden | 5.0 | [451] | Molecular, electronic structure |
| MolPro | 2012.1p22 | [452] | Quantum Chemistry, Ab Initio |
| mosaik | 2.1.33, 2.2.3 | [453] | Biology,NGS |
| Mothur | 1.36.1, 1.37.0, 1.38.1 | [454] | Biology, Microbial Ecology |
| MotionCorr | 2.1 | [455] | Motion Correction |
| MotionCor2 | 01302017 | [456] | Motion Correction |
| MOTU | 1.1 | [457] | Biology, Bioinformatics, Genomics |
| MOST | 20170721 | [458] | Biology, Genomics |
| MPE2 | 2.4.9b | [459] | MPI |
| MP-EST | 1.4, 1.5 | [460] | Biology, Phylogenetics |
| mpiP | 3.4.1 | [461] | Parallel Computing |
| MrBayes | 3.2.1, 3.2.4, 3.2.5 | [462] | Biology, Phylogenetics |
| MRIcron | 201306, 20161012 | [463] | Biology, MRI, Imaging |
| MUMmer | 3.23 | [464] | Biology, Genomics |
| MUSCLE | 3.8.31 | [465] | Biology, Genomics |
| MuTect | 1.1.4, 1.1.7 | [466] | Biology, Genomics |
| MutSig | 1.4, 1.41 | [467] | Biology, Genomics |
| MZMine | 2.19, 2.20, 2.21 | [468] | Biology, Spectroscopy |
| NAMD | 2.9, 2.11, 2.12 | [469] | Molecular Dynamics, Chemistry |
| Nanocorrect | 20150727 | [470] | Biology, NGS |
| Nanopolish | 20150904 | [471] | Biology |
| Nbody | 6 | [472] | Astronomy |
| NCBI C++ Toolkit | 12.0.0 | [473] | Biology, C++, Development |
| NCL | 6.1.2, 6.3.0 | [474] | Atmosphere Science |
| NCO | 4.2.1, 4.4.3 | [475] | Data exchange tools |
| Ncview | 2.1.2 | [476] | Data visualization |
| NeEstimator | 2.01 | [477] | Biology, Bioinformatics |
| NetCDF | 4.2, 4.3, 4.4.1.1 | [478] | Data exchange, Tools |
| NEURON | 7.4 | [479] | Biology, Neuroscience |
| Newbler | 2.7, 2.8, 2.9 | [480] | Biology, NGS |
| Newick utils | 1.6 | [481] | Biology, Phylogenetics |
| Nextallele | 20140718 | [482] | Biology, Genomics |
| NextGenMap | 0.5.3 | [483] | Biology, Bioinformatics, NGS |
| Nexus NCL | 2.1.18 | [484] | Biology, Phylogenetics, Library |
| NGS-bits | 0.1 | [485] | Biology, Sequencing |
| ngsCAT | 0.1 | [486] | Biology, Bioinformatics, NGS |
| ngsTools | 20150816 | [487] | Biology, NGS |
| NGSUtils | 20130722, 20150206 | [488] | Biology, NGS |
| Nipype | 0.10.0, 0.12.1, 0.13.1 | [489] | Biology, Bioinformatics, Neuroscience, Imaging |
| NMRPipe | 7.9 | [490] | Biology, Biochemistry |
| Novoalign | 2.08.02, 3.00.02 | [491] | Biology, NGS |
| NWChem | 6.5, 6.6 | [492] | Chemistry |
| NxTrim | 0.4.1 | [493] | Biology, Bioinformatics, NGS |
| Oases | 0.2.08 | [494] | Biology, NGS |
| OBITools | 1.2.11 | [495] | Biology, Phylogenetics |
| Olego | 1.1.2, 1.1.5, 1.1.6 | [496] | Biology, NGS, RNA-Seq |
| OCaml | 4.02.3 | [497] | Programming Languages, Scripting, Development |
| OCE | 0.18.1 | [498] | Library, 3D |
| Octave | 3.6.4 | [499] | Numerical Computation |
| Oncotator | 1.5.2.0, 1.5.3.0, 1.8.0.0 | [500] | Biology, Genomics |
| OpenBabel | 2.3.2, 2.4.1 | [501] | Biology, Chemistry |
| OpenCL | 1.1 | [502] | Programming, Library |
| OpenCV | 2.4.8 | [503] | Computervision |
| OpenFOAM | 2.1.1, 3.0.1, 4.0 | [504] | Fluid Dynamics |
| OpenMM | 6.2.0 | [505] | Quantum Chemistry |
| Orange3 | 3.3.6 | [506] | Data Mining, Visualization |
| OrthoFinder | 0.2.5, 0.6.0, 1.0.2 | [507] | Biology, Genomics |
| OrthoMCL | 2.0.2, 2.0.3, 2.0.7 | [508] | Biology, Genomics |
| OTB | 5.6.1 | [509] | Geospacial Imaging |
| p4vasp | 0.3.29 | [510] | Molecular, Electronic Structure |
| p53MH | 20020901 | [511] | Biology, Sequencing |
| Pacbio | 2.2.0, 2.3.0p5 | [512] | Biology, Bioinformatics, NGS |
| Package-GFE | 20150701 | [513] | Biology, Genomics |
| PALES | 122 | [514] | Physics |
| PALADIN | 1.3.1 | [515] | Biology, Phylogenetics |
| PAML | 4.7, 4.8a, 4.9a | [516] | Biology, Phylogenetics |
| Pandaseq | 20140808, 20150627 | [517] | Biology, Bioinformatics, NGS, Sequencing |
| PAPI | 5.1.0.2 | [518] | Software, Computing |
| Parallel | 20150122, 20170322 | [519] | Programming, Languages |
| ParaView | 4.1.0, 4.2.0, 4.3.0 | [520] | Data Analysis |
| Parsimonator | 1.0.2 | [521] | Biology, Bioinformatics |
| PartitionFinder | 1.1.1, 2.1.1 | [522] | Biology, Phylogenetics, Evolution |
| Parflow | v615 | [523] | Ecology, Modeling |
| PASA | 1.5, 2.0-r20150209 | [524] | Biology, Genomics |
| PASTA | 20160616 | [525] | Biology, Sequence alignment, |
| PAUP | 4.0b10, 4.1a147, 4.0a152 | [526] | Biology, Phylogenetics |
| PAUDA | 1.0.1 | [527] | Biology, Bioinformatics, Sequence alignment |
| PBalign | 20160921 | [528] | Biology, Bioinformatics |
| PBCore | 20151201 | [529] | Biology, Bioinformatics |
| PBCommand | 20151203 | [530] | Biology, Library |
| PBJelly | 14.7.14, 15.2.20, 15.8.24 | [531] | Biology, Bioinformatics |
| pbsdrmaa | 1.0.17 | [532] | Libraries, Torque |
| p4est | 1.1, 2.0 | [533] | Library |
| pbsmrtpipe | 20151202 | [534] | Biology |
| PeakSplitter | 1.0 | [535] | Biology, Chip-Seq |
| PEAR | 0.9.2, 0.9.6 | [536] | Biology, NGS |
| PECaller | 1.0.0 | [537] | Biology, NGS |
| PDT | 3.18, 3.20, 3.22 | [538] | Programming, Profiler |
| Perl | 5.16.0 | [539] | Programming, Language |
| PerM | 0.4.0 | [540] | Biology, NGS |
| PETSc | 2.3, 3.3 | [541] | Math, Numerical solvers |
| PGDSpider | 2.0.9.0 | [542] | Biology, NGS |
| PHAST | 1.4 | [543] | Biology, Phylogenetics |
| Phenix | 1.8.1069, 1.10.2155 | [544] | Crystallography |
| PHYLDOG | 20130418 | [545] | Biology, Genomics, Phylogenetics |
| Phyluce | 20140427, 20151103, 20160715 | [546] | Biology, Phylogenetics |
| Phyutility | 2.7.1 | [547] | Biology, Bioinformatics |
| Phyx | 0.99 | [548] | Biology, Phylogenetics |
| PfamScan | 1.3 | [549] | Biology, Genomics |
| PHITS | 2.52, 2.76. 2.82 | [550] | Physics |
| PHLAWD | 20170427 | [551] | Biology, Phylogenetics |
| Phonopy | 1.9.2 | [552] | Chemistry |
| PHYLIP | 3.696 | [553] | Biology, Phylogenetics |
| PhyloBayes | 3.3f, 1.4f MPI | [554] | Biology, Phylogenetics |
| PhyloNet | 3.5.7 | [555] | Biology, Phylogenetics |
| Phylosift | 1.1 | [556] | Biology, Genomics, Phylogenetics, Taxonomy |
| PhyML | 3.0, 3.1 | [557] | Biology, Phylogenetics |
| Picard | 2.0.1, 2.5.0, 2.9.2 | [558] | Biology, NGS |
| PICRUSt | 1.0.0, 1.1.0 | [559] | Biology, Phylogenetics |
| Pilon | 1.22 | [560] | Biology, Bioinformatics |
| PIPE-CLIP | 1.1.0 | [561] | Biology, NGS |
| Pipits | 1.3.6 | [562] | Biology, Sequencing |
| piPipes | 1.5.0 | [563] | Biology, Phylogenetics |
| Piranha | 1.2.1 | [564] | Biology, Phylogenetics |
| PLAST | 1.0 | [565] | Biology, Bioinformatics |
| Platypus | 0.8.1 | [566] | Biology, NGS |
| PLEK | 1.2 | [567]] | Biology, Phylogenetics |
| Plink | 1.07, 1.90b3, 1.90b3.39 | [568] | Biology, GWAS |
| PLINKSEQ | 0.10 | [569] | Biology, Genomics |
| PluMiST | 1.1 | [570] | Biology, Phylogenetics, Genomics |
| PolyPhen | 2.2.2.r405b | [571] | Biology, Genomics |
| PonyTools | 0.1 | [572] | Biology, Genomics |
| Poretools | 0.5.0 | [573] | Biology, Sequencing |
| POV-Ray | 3.7 | [574] | 3D, Graphics |
| Prank | 20150803 | [575] | Biology, Bioinformatics, Alignment |
| Preseq | 0.0.4 | [576] | Biology, NGS |
| PRICE | 1.2 | [577] | Biology, NGS |
| Primer3 | 2.3.4 | [578] | Biology, Genomics |
| PRIMUS | 1.8.0 | [579] | Biology, Phylogenetics |
| PRINSEQ | 0.20.4 | [580] | Biology, Sequencing |
| Prodigal | 2.6.3 | [581] | Biology, Genomics |
| ProfessAtQE | 2014 | [582] | Material Science, Molecular Dynamics |
| Prokka | 1.10, 1.11 | [583] | Biology, Genomics, Bioinformatics, Assembly |
| ProBABEL | 0.4.2, 0.4.3, 0.4.5 | [584] | Biology, Genomics, GWAS |
| Probalign | 1.4 | [585] | Biology, Genomics |
| Proovread | 1.03rcl | [586] | Biology, Genomics, NGS |
| Proteinortho | 4.26, 5.11, 5.16 | [587] | Biology, Genomics |
| PROVEAN | 1.1.5 | [588] | Biology, Genomics |
| PyAni | 0.2.1 | [589] | Bilogy, Genomics |
| PyHDF | 0.9.0 | [590] | Library, HDF4 |
| PyVCF | 0.6.0 | [591] | Biology |
| Python | 2.7.6, 3.5.0 | [592] | Biology, Genomics, NGS |
| Pyfasta | 0.5.2 | [593] | Biology, Phylogenetics |
| Pyrad | 3.0.63 | [594] | Biology, Sequencing Alignment, Assembly |
| QDD | 3.1.2 | [595] | Programming, scripting, language |
| QGIS | 2.18.0 | [596] | Geography |
| QIIME | 1.9.0, 1.9.1 | [597] | Biology, Ecology |
| QIIME2 | 2.0.6 | [598] | Biology, Ecology |
| QT | 4.8.3 | [599] | Computer Science |
| QUAST | 2.3, 4.4 | [600] | Biology, NGS |
| Quake | 0.3 | [601] | Biology, Sequencing |
| Quantas | 1.0.4, 1.0.8 | [602] | Biology, Bioinformatics, NGS |
| QualiMap | 2.1.1 | [603] | Biology, Sequence alignment |
| Quickquartet | 1.0.0 | [604] | Biology, Phylogenetics |
| R | Rmpi/3.3.1, 3.2.0, 3.3.0 | [605] | Statistics, Programming |
| R2R | 1.0.4 | [606] | Biology, RNA |
| R8S | 1.71, 1.8 | [607] | Biology, Evolution |
| Racon | 20161013 | [608] | Biology, Sequencing |
| RADICAL | 0.2 | [609] | Biology, Phylogenetics, Genomics |
| Randfold | 2.0.1 | [610] | Biology, RNA |
| Rascaf | 1.0.2 | [611] | Biology, RNA-Seq |
| RAxML | 8.2.3, 8.2.8, 8.2.10 | [612] | Biology, Phylogenetics |
| Ray | 2.3.1 | [613] | Biology, Genomics, NGS |
| REAGO | 1.1 | [614] | Biology, Assembly |
| REAPR | 1.0.18 | [615] | Biology, Bioinformatics, Assembly |
| Recycler | 0.62 | [616] | Biology, Bioinformatics |
| Regtools | 0.4.0 | [617] | Biology, RNA-seq |
| RELION | 1.4 | [618] | Biology, Bioinformatics |
| REPdenovo | 20170222 | [619] | Biology, Phylogenetics |
| RepeatExplorer | 20150506 | [620] | Biology, Genomics |
| RepeatMasker | 3.3.0 | [621] | Biology, Genomics |
| RepeatModeler | 1.0.8 | [622] | Biology, Bioinformatics |
| Reptile | 1.1 | [623] | Biology, NGS, error correction |
| RevBayes | 1.0.0, 1.0.3 | [624] | Biology, Phylogenetics |
| riboPicker | 0.4.3 | [625] | Biology, Sequence |
| RNAhybrid | 2.1.1 | [626] | Biology, Genomics |
| rRNASelector | 1.0.0 | [627] | Biology, Sequencing |
| rnaseqlib | 20150721 | [628] | Biology, Phylogenetics, RNA-Seq |
| rnaQUAST | 1.2.0 | [629] | Biology, NGS, Sequencing |
| ROOT | 6.0 | [630] | Data Analysis |
| Roary | 3.4.1 | [631] | Biology, Genomics |
| Rosetta | 2014wk4 | [632] | Biology, Structure, Modelling |
| RSEG | 0.4.8 | [633] | Biology, NGS |
| RSEM | 1.2.19, 1.2.28, 1.2.29 | [634] | Biology, NGS, RNA-Seq |
| RSeQC | 2.3.7, 2.6.2 | [635] | Biology, NGS, RNA-Seq |
| RStudio | 0.99.902, 0.99.903 | [636] | R, Statistics, Programming |
| RTGTools | 3.7.1 | [637] | Biology, NGS |
| Ruby | 1.9.3-p0 | [638] | Programming, Scripting, Language |
| Sailfish | 0.6.3 | [639] | Biology, NGS, RNA-Seq |
| Salmon | 0.6.0, 0.7.2 | [640] | Biology, RNA-seq |
| SMC++ | 1.7.0 | [641] | Biology, NGS |
| Sambamba | 0.5.0-dev, 0.5.10, 0.6.3 | [642] | Biology, NGS |
| Samstat | 1.08 | [643] | Biology, NGS, Bioinformatics, Sequencing |
| Samblaster | 0.1.14 | [644] | Biology, NGS |
| samtools | 1.1, 1.2, 1.3.1 | [645] | Biology, NGS |
| SAS | 9.3 | [646] | Statistics, Graphing |
| SATe | 2.2.7 | [647] | Biology, Phylogenetics |
| Scala | 2.11.5 | [648] | Programming, Language |
| Scalablast | 2.4.53 | [649] | Biology, Genomics |
| Scalpel | 0.1.1, 0.5.3 | [650] | Biology, NGS |
| SCRIPTURE | 20101211 | [651] | Biology, Bioinformatics, Genomics |
| Shannon | 20160211 | [652] | Biology, RNA-Seq |
| SHAPEIT | 2.5.5 | [653] | Biology, SNP |
| SHAPE-MaP | 1.2 | [654] | Biology, Phylogenetics |
| Sharcgs | 1.2.11 | [655] | Biology, NGS, Assembly |
| SHEsisPlus | 1.0 | [656] | Biology, Phylogenetics |
| shustring | 2.6 | [657] | Biology, Sequencing |
| SCons | 2.3.0 | [658] | Programming |
| Scoary | 1.6.10 | [659] | Biology, Bioinformatics, Genomics |
| SCRATCH1D | 1.0 | [660] | Biology, Genomics |
| Scythe | 0.991 | [661] | Biology, NGS |
| SDT | 1.2 | [662] | Biology, Sequencing |
| Segemehl | 0.1.9 | [663] | Biology, NGS, Mapper |
| SEPP | 1.0, 3.0 | [664] | Biology, Phylogenetics, HMM |
| SGA | 0.10.14 | [665] | Biology, Assembly |
| Seq-Gen | 1.3.3 | [666] | Biology, Phylogenetics |
| SeqPrep | 0.5 | [667] | Biology, NGS |
| Seqmagick | 20150923 | [668] | Biology, Phylogenetics |
| SeqMap | 1.0.13 | [669] | Biology, NGS |
| Seqtk | 20140729 | [670] | Biology, NGS |
| SEQuel | 1.0.1 | [671] | Biology, NGS |
| SeqyClean | 1.8.10 | [672] | Biology, NGS, Bioinformatics |
| ShoRAH | 20131204 | [673] | Biology, NGS, quality filter |
| SHRiMP | 2.2.3 | [674] | Biology, NGS |
| SICER | 1.1 | [675] | Biology, ChIP-Seq |
| Sickle | 1.200, 1.33 | [676] | Biology, NGS, quality filter |
| Siesta | 2.0.2,3.1 | [677] | Simulation, Physics, Ab Initio |
| Sisl | 0.8.3 | [678] | Physics, Tight-binding |
| SIFT | 4.0.3b | [679] | Biology, Genomics |
| SignalP | 4.1c | [680] | Biology, NGS |
| Silo | 4.7 | [681] | Library, Data |
| SIPeS | 2.0 | [682] | Biology, Bioinformatics, ChIP-Seq |
| Slicer | 4.3.1 | [683] | Biology, Imaging |
| SMALT | 0.7.6 | [684] | Biology, NGS |
| Snap | 20100728, 0.15.4 | [685] | Biology, Genomics |
| SNAPE-pooled | 20130407 | [686] | Biology, SNP |
| SNeP | 1.1 | [687] | Biology, Phylogenics |
| SnpEff | 4.2, 4.3, 4.3p | [688] | Biology, NGS, Genomics |
| SNPhylo | 20140701 | [689] | Bilogy, Phylogenetics |
| SNP-sites | 2.0.3 | [690] | Biology, SNP |
| Snippy | 20160419 | [691] | Biology, Phylogenetics |
| SOAPdenovo | 1.05 | [692] | Biology, NGS |
| SOAPdenovo-Trans | 1.01, 1.03 | [693] | Biology, NGS |
| SOAPec | 2.03 | [694] | Biology, Phylogenetics |
| SOAPsplice | 1.10 | [695] | Biology, NGS |
| SortMeRNA | 2.1 | [696] | Biology, Sequencing, NGS |
| SparCC | 201402 | [697] | Microbial Ecology |
| Spades | 3.9.0, 3.10.0, 3.10.1 | [698] | Biology, NGS |
| Spanki | 0.4.1, 0.4.3, 0.5.0 | [699] | Biology, NGS, RNA-Seq |
| SPARTA+ | 2.60 | [700] | Chemistry |
| Spidey | 20150922 | [701] | Biology, Genomics |
| SPIMAP | 1.1 | [702] | Biology, Phylogenetics |
| SpliceTrap | 0.90.5 | [703] | Biology, NGS, RNA-Seq |
| SPM | 8 | [704] | Biology, Statistics, Neurology, Imaging |
| Sputnik | 1.0 | [705] | Biology, Genomics |
| SQLite | 3.8.8.2 | [706] | Database |
| SQL_Developer | 4.1.2 | [707] | Programming, Oracle, Sql |
| SRA | 2.1.10 | [708] | biology, NGS |
| SSPACE | 2.0, 3.0 | [709] | Biology, NGS |
| SST-Core | 6.0.0 | [710] | MPI |
| SSR_pipeline | 0.951 | [711] | Bilogy, DNA Sequencing |
| Stacks | 1.24, 1.35, 1.45 | [712] | Biology, Genomics, NGS |
| Staden | 1.14.6 | [713] | Biology, Sequencing |
| Stampy | 1.0.31 | [714] | Biology, Bioinformatics, Sequencing |
| STAR | 2.4.0j, 2.5.1b | [715] | Biology, NGS, Alignment |
| STAR-CCM+ | 8.06 | [716] | Mechanical Engineering |
| Stata | 10.1, 13 | [717] | Statistics, Data analysis |
| Statsmodels | 0.8.0 | [718] | Biology, Library, Math |
| Stringtie | 1.1.2, 1.2.1, 1.3.3 | [719] | Biology, NGS, Alignment |
| Structure | 2.3.3, 2.3.4 | [720] | Biology, Population |
| stringMLST | 0.4 | [721] | Biology, Genomics, NGS |
| Subread | 1.5.0-p1, 1.5.1 | [722] | Biology, Sequencing, SNP |
| Supercell | 20170602 | [723] | Biology, NGS |
| Supernova | 1.1.5 | [724]] | Biology, Phylogeneitcs, NGS |
| SUNDIALS | 2.3.0, 2.5.0 | [725] | Numerical Solver |
| SVDetect | 0.8b | [726] | Biology, NGS, SNP |
| swak4Foam | 2.x | [727] | Fluid Dynamics |
| swarm | 1.2.11 | [728] | Data Analysis |
| SWEEP | 20160722 | [729] | Biology, SNP |
| Swig | 2.0.9 | [730] | Programming, C, C++, Python |
| SwitchSeq | 20140907 | [731] | Biology, NGS |
| Syzygy | 1.2.7 | [732] | Biology, Genomics |
| TetGen | 1.5.0 | [733] | Tetrahedral Meshes 3D |
| tapir | 20160825 | [734] | Biology, Phylogenetics |
| TAPIS | 1.2.1 | [735] | Biology, Sequencing |
| TASSEL | 5.0, 5.2.29 | [736] | Biology, Genomics |
| TAU | 2.21.4, 2.23, 2.24, 2.52 | [737] | Profiling, Tracing, Programming |
| taxMap | 0.1 | [738] | Biology, Phylogenetics, Taxonomy |
| TaxonDNA | 1.8 | [739] | Biology, Taxonomy |
| T-Coffee | 9.03.r1318 | [740] | Biology, Genomics, Multiple Alignment |
| TEToolkit | 1.5.1 | [741] | Biology, Bioinformatics, Sequencing |
| TensorFlow | 1.0.0, 1.2.0 | [742] | Library, Math |
| TESS | 2.3.1 | [743] | Biology, Genomics, Markov |
| tgicl | 2.1 | [744] | Biology, sequencing, clustering |
| Tmux | 2.0 | [745] | GNU, Terminal Multiplexer |
| TomoPy | 0.0.3 | [746] | Biology, Neuroimaging |
| Tophat | 1.4.1, 2.0.13, 2.1.0 | [747] | Biology, NGS |
| Torch | 20160704, 20171102 | [748] | Lua |
| Totalview | 8.12.0 | [749] | Computer Science |
| TPP | 4.7.0 | [750] | Bioinformatics, MassSpec |
| TrackTools | 2011 | [751] | Bioinformatics |
| TrackVis | 0.5.2.2 | [752] | Biology, Spectroscopy |
| Tracula | 5.3.2014_05_26 | [753] | Biology, Bioinformatics, Neuroscience, Imaging |
| TraitRate | 1.1 | [754] | Biology, Evolution |
| Trans-ABySS | 1.5.4 | [755] | Biology, Phylogenetics |
| TransDecoder | 20140704, 2.0.1, 3.0.0 | [756] | Biology, NGS |
| Transrate | 1.0.1 | [757] | Biology, Assembly |
| TransVar | 2.3.3 | [758] | Biology, Phylogenetics |
| TraCeR | 20160519 | [759] | Biology, Bioinformatics |
| TreeCorr | 3.2.3 | [760] | Physics |
| TreeFix | 1.1.7, 1.1.10 | [761] | Biology, Phylogenetics |
| TreeMix | 1.12 | [762] | Biology, Phylogenetics |
| TreePL | 20150305 | [763] | Biology, Phylogenetics |
| TREEPUZZLE | 5.3 | [764] | Biology, Phylogenetics |
| TriMetAss | 1.1 | [765] | Biology, Bioinformatics, NGS |
| TRF | 4.04 | [766] | Biology, Genomics |
| Trilinos | 11.4.1, 11.8.1 | [767] | Math Algorithm |
| trimAl | 1.2 | [768] | Biology, Genomics, Sequence Alignment |
| Trim Galore | 0.2.8, 0.4.1, 0.4.4 | [769] | Biology, NGS |
| Trimmomatic | 0.32, 0.33, 0.36 | [770] | Biology, NGS |
| Trinity | r20161120-2.3.2, r20170205-2.4.0 | [771] | Biology, NGS, RNA-Seq |
| Trinotate | 2.0.1, 3.0.1 | [772] | Biology |
| TRNAscan-SE | 1.23 | [773] | Biology, NGS, Bioinformatics |
| Twinscan | 4.1.2 | [774] | Biology, Genomics |
| usearch | 7.0.1001-64, 8.0.1517, 9.2.64 | [775] | Biology, Sequence analysis |
| UDUNITS | 2.2.17 | [776] | Library, Units, Programming |
| UFITS | 0.7.2 | [777] | Biology, NGS |
| UNAFold | 3.8 | [778] | Biology, Genome, RNA, Folding |
| UProC | 1.2.0 | [779] | Biology, Genomics |
| Valgrind | 3.9.0 | [780] | Computer Science |
| VarDictJava | 20160521 | [781] | Biology, NGS |
| Varnorm | 0.21 | [782] | Biology, Phylogenetics |
| VarScan | 2.3.6 | [783] | Biology, NGS, Genomics |
| VASP | 5.3.2, 5.3.3, 5.3.5, 5.4.1 | [784] | Quantum Chemistry, Ab Initio |
| VAST-TOOLS | 20150506 | [785] | Biology, NGS, RNA-Seq |
| VCFLib | 20141119, 20150313 | [786] | Biology, NGS, Genomics |
| VCFtools | 0.1.12a, 0.1.12b, 0.1.14 | [787] | Biology, SNPs |
| velvet | 1.2.06, 1.2.07, 1.2.10 | [788] | Biology, Genomics, NGS |
| VEP | 74, 83 | [789] | Biology, NGS |
| VICUNA | 1.3 | [790] | Biology, Assembly |
| ViennaRNA | 2.2.6 | [791] | Biology, RNA-seq |
| Vim | 7.4.5 | [792] | Programming, Scripting, Language |
| vmd | 1.9.1, 1.9.3 | [793] | Biology, Visualization |
| VSearch | 20151022, 20161209-2.3.4 | [794] | Biology, NGS |
| VT | 20140903, 20160129 | [795] | Biology, Genomics |
| VTC | 0.9.3 | [796] | Biology, Bioinformatics, VCF |
| VTK | 6.1.0 | [797] | Visualization, Graphics |
| V-Phaser2 | 02112013 | [798] | Biology, Phylogenetics |
| Virsorter | 1.0.3 | [799] | Biology, Phylogenetics |
| w2rap-contiger | 20161124 | [800] | Biology, Genomics |
| Wannier90 | 1.2, 2.0.0 | [801] | Computational Physics |
| WebLogo | 3.3, 3.5.0 | [802] | Biology, Genomics |
| WEVOTE | 1.5.0, 1.8.0 | [803] | Biology, Genomics |
| WDSSII | 1 | [804] | Meteorology |
| WIEN2k | 12.1 | [805] | Material Science, Chemistry |
| Wgs or Celera | 8.2, 8.3rc1, 8.3rc1.r4638 | [806] | Biology, NGS |
| wublast | 2.0 | [807] | Biology, Sequence Alignment |
| YAHA | 0.1.82 | [808] | Biology NGS |
| Xander | 20151222 | [809] | Biology, Phylogenetics |
| XCrySDen | 1.5.60 | [810] | Computational Material Science |
| Yambo | 3.3.0 | [811] | Physics |
| YASM | 1.3.0 | [812] | Computer Science |
| Yasra | 2.32 | [813] | Biology, NGS |
| Zagros | 1.0.0 | [814] | Biology, NGS |
| Zeo++ | 0.2.2 | [815] | Chemistry |
| Zorro | 2.2 | [816] | Biology, Sequencing |
- ↑ Up to 3 most recent/important releases are listed. See the individual application pages and the output of "module spider software" for full version listing.
Add New App
To add a documentation page for a new piece of software installed into /apps please go to Add New App Page.