Difference between revisions of "Installed Software"
Jump to navigation
Jump to search
Line 46: | Line 46: | ||
|- | |- | ||
| [[AMPtk]] || 0.8.0, 0.8.5 || [https://github.com/nextgenusfs/amptk] || Biology, Bioinformatics, NGS | | [[AMPtk]] || 0.8.0, 0.8.5 || [https://github.com/nextgenusfs/amptk] || Biology, Bioinformatics, NGS | ||
+ | |- | ||
+ | | [[ANGEL]] || 2.3 || [https://github.com/PacificBiosciences/ANGEL] || Biology, Bioinformatics, NGS | ||
|- | |- | ||
| [[Anvio]] || 2.0.0, 2.0.2, 2.1.0 || [https://github.com/meren/anvio] || Biology, Microbial 'omics | | [[Anvio]] || 2.0.0, 2.0.2, 2.1.0 || [https://github.com/meren/anvio] || Biology, Microbial 'omics |
Revision as of 20:18, 2 May 2017
- Last updated on 2017-05-02.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 |
---|---|---|---|
4P | 1.0 | [1] | Biology, SNP |
AbInit | 6.12.3, 7.10.2, 7.10.4 | [2] | Quantum Chemistry, DFT |
Abyss | 1.5.2, 1.9.0, 2.0.0 | [3] | Biology, NGS |
ADMB | 11.5 | [4] | Math, Modeling, Optimization |
AdmixTools | 20150311, 20160513 | [5] | Biology, Bioinformatics, Genomics, NGS |
ADMIXTURE | 1.23, 1.3.0 | [6] | Biology, Bioinformatics, Genomics, NGS |
AEGeAn | 0.14.0 | [7] | Biology, Genomics |
AFNI | 2013_11_24, 2016_0_19 | [8] | Biology, Statistics, Imaging, Neurology |
Agalma | 0.2.1, 0.3.5, 0.5.0 | [9] | Biology, Bioinformatics, Genomics, SNP |
AGOUTI | 0.3.3 | [10] | Biology, Genomics |
ALE | 20150507 | [11] | Biology, Bioinformatics, Assembly |
ALLPATHS-LG | 42316, 44837 | [12] | Biology, NGS |
Amber | 11, 12, 14, 16 | [13] | Simulation, chemistry |
AMAS | 0.98 | [14] | Biology, Sequence Alignment |
AMOS | 3.1.0 | [15] | Biology, Genomics, NGS |
AMPHORA2 | 20140305 | [16] | Biology, Phylogenetics |
AMPtk | 0.8.0, 0.8.5 | [17] | Biology, Bioinformatics, NGS |
ANGEL | 2.3 | [18] | Biology, Bioinformatics, NGS |
Anvio | 2.0.0, 2.0.2, 2.1.0 | [19] | Biology, Microbial 'omics |
ANNOVAR | 20120621, 20150322 | [20] | Biology, Genomics |
AStalavista | 3.2 | [21] | Biology, NGS, RNA-Seq, Genomics |
ASTRID | 20150807 | [22] | Biology, Genomics |
Atlas | 3.10.1, 3.11.17 | [23] | Library, Math |
Amuse | 6.0, 10.0 | [24] | Astrophysics |
ANGSD | 20150306, 20150909 | [25] | Biology, NGS |
Affymetrix Power Tools | 1.15.0, 1.18.0 | [26] | Biology, Genomics, Microarray |
ArrayFire | 3.4.2 | [27] | Code Optimization |
ARC | 20140312 | [28] | Biology, NGS |
ARCS | 1.0.0, 1.0.1 | [29] | Biology, Genomics |
Armadillo | 6.200.3 | [30] | Library, C++ , Math |
Astral | 4.10.6, 4.10.7, 5.0.3 | [31] | Biology, Bioinformatics, NGS, Phylogenetics |
AtomEye | 3 | [32] | Material Science |
ATRAM | 20140624 | [33] | Biology, NGS |
Augustus | 2.6, 3.2.1, 3.2.2 | [34] | Biology, NGS |
Auto3DEM | 4.05.1, 4.05.2 | [35] | Image Reconstruction |
BamBam | 1.0 | [36] | Biology, NGS |
BALI-PHY | 2.3.8 | [37] | Bioinformatics, Bayesian Estimation |
BAMM | 2.5.0 | [38] | Biology, Phylogenetics |
Bam-readcount | 20150216 | [39] | Biology, NGS |
Bamstats | 20140602 | [40] | Biology, NGS |
Bamtools | 2.1.1 | [41] | Biology, NGS |
BamUtil | 1.0.2 | [42] | Biology, NGS |
Bam-Readcount | 20150616 | [43]] | Biology, Genomics |
BAPS | 6.0 | [44] | Biology, Populaton genetics |
Barrnap | 0.7 | [45] | Biology, RNA-Seq |
Basemount | 0.1.2.464 | [46] | Biology, DNA Sequencing |
BatVI | 1.00 | [47] | Biology, Phylogenetics |
BayArea | 1.0.2 | [48] | Biology |
BayeScan | 2.1 | [49] | Biology, SNP |
BayeScEnv | 1.1 | [50]] | Biology, SNP, Phylogenetics |
BayesRate | 1.3.43 | [51] | Biology, Phylogenetics |
Bbcp | 12.08.17.00.0 | [52] | Network file transfer |
BBMap | 36.23, 37.09 | [53] | Biology, Alignment |
Bcbio-nextgen | 0.8.7, 0.9.9 | [54] | Biology, NGS |
Bcftools | 1.2, 1.3.1, 1.4 | [55] | Biology, Genomics, NGS |
Bcl2fastq | 2.16 | [56] | Biology, NGS, Illumina |
BEAGLE | 3.2.2, 4.0 | [57] | Biology, Genetics, Genotyping |
BEAST | 1.7.5, 1.8.1, 2.3.2 | [58] | Biology, Phylogenetics |
Bedops | 2.4.2 | [59] | Biology, Bioinformatics, Sequence, NGS |
BEDTools | 2.23.0, 2.24.0, 2.26.0 | [60] | Biology, NGS |
BEST | 2.3.1 | [61] | Biology, Phylogenetics |
BESST | 2.2.4 | [62] | Biology, Bioinformatics |
BETA | 1.0.5 | [63] | Biology, NGS |
BFAST | 0.7.0 | [64] | Biology, NGS |
Bismark | 0.7.7, 0.13.0, 0.17.0 | [65] | Biology, NGS, Methylation |
BinPacker | 1.0 | [66] | Biology, RNA-Seq, Sequence Assembly |
BinSanity | 0.1.3 | [67] | Biology, Genomics |
Bioconductor | Latest | [68] | Biology, R, Statistics |
BioPerl | 1.006901 | [69] | Biology, Perl |
BioPython | 1.59 | [70] | Biology, Python |
BLASR | 20130815 | [71] | Biology, NGS |
NCBI BLAST | 2.2.27, 2.5.0, 2.6.0 | [72] | Biology, Sequence alignment |
Blast2go | 2.5.0-20120705 | [73] | Biology, Annotation |
BLAT | 20120524, 20140318 | [74] | Biology, Sequence alignment |
Blender | 2.63 | [75] | Graphics |
BLESS | 1.02 | [76] | Biology, NGS |
BLUPF90 | 20160604 | [77] | Biology, Phylogenetics |
BoltzTraP | 1.2.5 | [78] | Physics |
Boost | 1.49.0, 1.59.0, 1.63.0 | [79] | C++, Library |
Bowtie | 0.12.9, 1.1.1, 1.2.0 | [80] | Biology, NGS |
Bowtie2 | 2.2.8, 2.2.9, 2.3.0 | [81] | Biology, NGS |
BPP | 1.9.0, 2.2, 3.2 | [82] | Biology, Phylogenetics |
Bracken | 1.0.0 | [83] | Biology, Phylogenetics |
BRANCH | 1.8.1 | [84] | Biology, NGS, Mapping |
BRATNextGen | 20150505 | [85] | Biology, Genomics |
BRIG | 0.95 | [86] | Biology, Genomics |
Bsoft | 1.9.1 | [87] | Biology, Image Analysis |
Bsmap | 2.74, 2.87 | [88] | Biology, NGS, Methylation |
BSSeeker2 | 2.1.0 | [89] | Biology, Phylogenetics |
BUCKy | 1.4.4 | [90] | Biology, Genomics |
BUSCO | 1.1b1, 1.22, 2.0b | [91] | Biology, Genomics |
Bwa | 0.6.1, 0.7.12, 0.7.15 | [92] | Biology, NGS |
BXH_XCEDE_tools | 1.11.1 | [93] | Biology, Bioinformatics |
Camino | 20140723 | [94] | Biology, Neuroscience, Imaging |
Canu | 1.1, 1.3, 1.5 | [95] | Biology, Sequencing |
CASM | 0.2.0 | [96] | Statistical Mechanics |
CAP3 | 20120705 | [97] | Biology, Sequence Assembly |
CASAVA | 1.8.2 | [98] | Biology, NGS |
CD-HIT | 4.6, 4.6.4 | [99] | Biology, Genomics |
CDO | 1.6.1, 1.7.2rc5 | [100] | Climate |
CEAS | 1.0.2 | [101] | Biology, Genomics |
CellProfiler | 2.0 | [102] | Biology, Image Analysis |
CellRanger | 1.2.1, 1.3.0 | [103] | Biology, Bioinformatics, NGS, RNA-Seq |
CFITSIO | 3.370 | [104] | Library, C |
CGATools | 1.6.0.42 | [105] | Biology, NGS |
Charmm | 36a3 | [106] | Simulation, Chemistry |
Chartdirector | 5.1.0 | [107] | Graphics |
CheckM | 1.0.4 | [108] | Biology, Genomics |
Chimera | 1.7 | [109] | Biology, Modeling |
ChromEvol | 2.0 | [110] | Biology, Phylogenetics |
CIMS | 4.1.2 | [111] | Biology, Genomics |
Circos | 0.63-pre11, 0.69-2 | [112] | Biology, Visualization |
CisGenome | 2.0 | [113] | Biology, Genomics, Peak Calling |
Clann | 3.2.3 | [114] | Biology, Phylogenetics |
CLARK | 1.2.2-b | [115] | Biology, Genomics |
CLHEP | 2.2.0.1 | [116] | High Energy Physics |
CLIPper | 1.0 | [117] | Biology, Sequencing |
CLIPSeqTools | 0.1.7 | [118] | Biology, Sequencing |
ClonalFrame | 1.1, 1.2 | [119] | Biology, Genomics, NGS |
ClonalFrameML | 1.25 | [120] | Biology, Genomics, NGS |
ClustalW | 2.1 | [121] | Biology, Genomics |
Cluster3 | 1.52 | [122] | Biology, Genomics |
Clview | 20130402 | [123] | Biology, Genomics |
ClustalO | 1.2.0 | [124] | Biology, Genomics |
CLUMPP | 1.1.2 | [125]] | Biology, Bioinformatics |
ClusterFinder | 313 | [126] | Biology, Metabolomics |
CMake | 2.8.8, 2.9.12.1, 3.1.0 | [127] | Programming, Build System |
CMWP | 140518 | [128] | Biology, Genomics |
CNVnator | 0.3.2 | [129] | Biology, Genomics |
CNVSeq | 20110715 | [130] | Biology, NGS |
Cobrapy | 0.3.2 | [131] | Biology, Metabolomics, Modeling |
Coevol | 1.3c, 1.4b | [132] | Biology, Phylogenetics |
CoMap | 1.4.1 | [133] | Biology, Genomics |
CONSEL | 0.20 | [134] | Biology, Phylogenetcs |
CONCOCT | 0.3.1 | [135] | Biology, Genomics |
ContaVect | 0.2 | [136] | Biology, Phylogenetics |
CoNIFER | 0.2.2 | [137] | Biology, Genomics |
Consed | 23.0 | [138] | Biology, Genomics |
Coreutils | 8.23 | [139] | GNU Utilities, Computer Science |
Corset | 1.06 | [140] | Biology, NGS |
covNMR | 2014 | [141] | Biochemistry |
CPLEX | 12.6.5 | [142] | Optimizer |
CUDA | 4.2, 5.5 | [143] | Programming, Graphics |
Crass | 1.0.1 | [144] | Biology, Assembly |
CRISPRdigger | 1.007 | [145] | Biology, Phylogenetics |
CrossMap | 0.2.3 | [146] | Biology, Genomics |
Crux | 1.40 | [147] | Biology, Mass-Spectrometry |
Cufflinks | 1.3.0, 2.0.2, 2.2.1 | [148] | Biology, NGS |
Cutadapt | 1.7.1, 1.8.1, 1.10 | [149] | Biology, NGS |
CUTE | 20160116, 20161010 | [150] | Cosmology |
Cytoscape | 3.4.0 | [151]] | Biology, Bioinformatics |
DAKOTA | 5.4.0 | [152] | Computational Science |
DaPars | 0.9.0 | [153] | Biology, NGS, RNA-Seq |
DALIGNER | 1.0 | [154] | Biology, Sequencing |
Datamash | 1.1.0 | [155] | Math |
DCMTK | 3.6.0 | [156] | Biology, Neuroscience, Imaging |
DSSAT | 4.5 | [157] | Biology |
dDocent | 20160425 | [158] | Biology |
DDSCAT | 7.3.0 | [159] | Astrophysics |
DDT | 4.1.0, 4.2.1 | [160] | Software |
Dealii | 8.3.0, 8.4.1 | [161] | Library |
DeconSeq | 0.4.3 | [162] | Biology, Phylogenetics |
Delft3D | 3621 | [163] | Hydrodynamics, Physics |
DeepPicker | 20161102 | [164] | Deep Learning, Cross-Molecule Training |
DeepTools | 2.4.3 | [165] | Biology, Bioinformatics, NGS |
Desmond | 3.0.3.1 | [166] | Simulation, Biology, Chemistry |
DETONATE | 1.9, 1.11 | [167] | Biology, NGS |
DEXTRACTOR | 1.0 | [168] | Biology, Sequencing |
Dalton | 2011 | [169] | Quantum Chemistry |
Diamond | 0.5.1, 0.8.5 | [170] | Computational Biology, Genomics |
Dibig Tools | 1.0 | [171] | Bioinformatics, PBS, Torque, Jobs |
DiffReps | 1.55.4 | [172] | Biology, NGS, ChIP-Seq |
Dindel | 1.01 | [173] | Biology, NGS |
DISCOVARdenovo | 52488 | [174] | Biology, NGS |
DIYABC | 1.0.4.43b, 2.0.3 | [175] | Biology, Genomics |
Dlpoly | 4.03.4 | [176] | Simulation, Biology, Chemistry |
Dlpoly-Classic | 1.9 | [177] | Simulation, Biology, Chemistry |
DNA Clust | 3.0 | [178] | Biology, Genomics |
Dock | 6.5, 6.6, 6.7 | [179] | Chemistry, ligand binding prediction |
DOT | 2.0 | [180] | Biology, Bioinformatics, Docking |
DosageConvertor | 1.0.3 | [181] | Biology, Converter |
Doxygen | 1.8.3.1 | [182] | Programming, Documentation |
DSSP | 2.2.1 | [183] | Biology, Molecular Dynamics |
DTI-TK | 2.3.1 | [184] | Biology, Neurology, Imaging |
EA-Utils | 1.1.2.537 | [185] | Biology, NGS |
ECTools | 20140311, 20141201 | [186] | Biology, Sequencing, Bioinformatics |
ECE | 1.0 | [187] | Ece |
EEGLAB | 12.0.2.1b, 13.2.2b, 13.4.4b | [188] | Biology, Matlab |
ED2 | 2.1 | [189] | Biology |
eGene-MVN | 0.1 | [190] | Biology, Genetics |
eigenMT | 20160228 | [191] | Biology, Genetics |
EIGENSOFT | 4.2, 5.0.1, 6.0.1 | [192] | Biology, Population |
emboss | 6.5.7 | [193] | Biology, multi-tool suite |
EMAN2 | 2.11 | [194] | Biology |
EMMAX | 20100307, 20120210 | [195] | Biology, NGS, Mapping |
EMC | 9.3.9 | [196] | Monte Carlo Simulations |
EMIRGE | 20130727 | [197] | Biology, NGS |
Ensembl_Tools | 80 | [198] | Biology, Bioinformatics |
EPACTS | 3.2.6 | [199] | Biology, Bioinformatics, Genomics |
EPOCH | 4.7.3 | [200] | Astronomy, CPPP |
eQTLA | 1.1 | [201] | Biology, Genomics |
Eqtlbma | 1.2.2 | [202] | Biology, Genotyping |
Esmf | 6.3.0rp1 | [203] | Climate |
Espresso | 5.0.1, 5.2.0, 5.2.1, 5.3.0 | [204] | Modeling, Physics |
ESPRIT | 201211 | [205] | Biology, NGS, Metagenomics |
ETE2 | 2.1 | [206] | Biology, Phylogenetics |
ETE3 | 3.0.0 | [207] | Biology, Phylogenetics |
Eval | 2.2.8 | [208] | Biology, Genomics, GUI |
ExaBayes | 1.4.1, 1.5 | [209] | Biology, Phylogenetics |
ExaML | 1.0.5, 1.0.12, 3.0.14, 3.0.17 | [210] | Biology, Phylogenetics |
ExomeCNV | 1.4 | [211] | Biology, NGS, Genomics |
Exonerate | 2.2.0 | [212] | Biology, Genomics |
eXpress | 1.3.1 | [213] | Biology, NGS |
FALCON | 20160828, 20161222 | [214] | Biology, Bioinformatics, NGS, Sequencing |
FALCON_unzip | 20160623, 20161222 | [215] | Biology, Bioinformatics |
FAR | 2.15 | [216] | Biology, Genomics |
FASTA | 34.26.5, 36.3.6d | [217] | Biology, Genomics |
FAST-iCLIP | 0.9.1 | [218] | Biology, Sequencing |
FastML | 3.0 | [219] | Biology, Phylogenetics, ML |
FastQC | 0.10.1, 0.11.2, 0.11.4 | [220] | Biology, NGS |
Fastq-tools | 0.7, 0.8 | [221] | Biology, NGS |
FastStructure | 20150112 | [222] | Biology, Genomics |
FastTree | 2.1.7 | [223] | Biology, Phylogenetics |
Fastx_toolkit | 0.0.13.2 | [224] | Biology, NGS |
Fathmm | 20150225 | [225] | Biology, Genomics |
fcGENE | 1.0.7 | [226] | Biology, Genomics, SNP |
Ferret | 6.82 | [227] | Oceanography, Meteorology |
FFmpeg | 2.1.3, 2.8.3 | [228] | Multimedia, audio, video |
FFTW | 3.3.2, 3.3.3, 3.3.4 | [229] | Math, Library, C++ |
FineSTRUCTURE | 2.0.7 | [230] | Biology, Populatiopn Genetics |
FLASH | 1.2.10, 1.2.11 | [231] | Biology, Genomics, NGS |
Flexbar | 2.3 | [232] | Biology, Genomics, NGS |
Fluent | 14.5.7, 15.0.7, 16.0, 17.2 | [233] | Simulation, Fluid Dynamics |
fqtools | 20160224 | [234] | Biology, Bioinformatics, NGS |
FragGeneScan | 1.16 | [235] | Biology, NGS, Genomics |
FrameDP | 1.2.2 | [236] | Biology, Sequencing |
Frealign | 9.11 | [237] | Image Reconsctruction |
FreeBayes | 1.0.1, 1.0.2, 1.1.0 | [238] | Biology, NGS, SNP Calling |
FREEC | 9.6 | [239] | Biology, Sequencing |
Freesurfer | 5.2.0, 5.3.0 | [240] | Biology, Neurology, Imaging |
FSL | 5.0.2.2 | [241] | Biology, Neurology, Imaging |
Galaxy | latest | [242] | Biology, Chemistry, Other |
GapFiller | 1.11 | [243] | Biology, NGS |
Garli | 2.0, 2.01 | [244] | Biology, Phylogenetics |
GAML | 20150610 | [245] | Biology, NGS |
GAMBIT | 15.1.0, 16.0.0 | [246] | Game Theory |
GARM | 0.7.4 | [247] | Biology, NGS |
GASVPro | 201310 | [248] | Biology, NGS, Genomics |
GATE | 7.0 | [249] | Data Analysis |
GATK | 1.6.9, 3.4.46, 3.5.0 | [250] | Biology, NGS |
Gaussian | G03, G09-A.02, G09-C.01 | [251] | Modeling, Computational Chemistry |
Gblocks | 0.91b | [252] | Genomics, Alignment tool |
GCTA | 1.24.7, 1.26.0 | [253] | Biology, Genomics, SNP |
GDAL | 1.11.2 | [254] | Geospatial Data Modeling, Geospatial Library |
GDC-Client | 1.0.1 | [255] | Biology, Bioinformatics, Sequencing, NGS |
Geant4 | 4.10 | [256] | Physics |
GEM | 20130406 | [257] | Biology, NGS |
gem5 | 2.0 | [258]] | Computer Simulator |
GEMINI | 4.6.6a, 0.13.1, 0.18.0 | [259] | Biology, Genomics, Genetics |
GenBank Tools | 20140130 | [260] | Biology, Genomics |
GeneMark | 2012.04 | [261] | Biology, Genomics, Metagenomics |
GeneSeqer | 20140226 | [262] | Biology, Genomics |
Genewise | 2.2.0 | [263] | Biology, Genomics, Annotation |
Genome STRiP | 2.00.1602 | [264] | Biology, genomics, NGS |
GenomicConsensus | 20160523 | [265] | Biology, Phylogenetics |
GenomicTools | 2.7.0 | [266] | Biology, NGS |
GenomeTools | 1.5.7 | [267] | Biology, Bioinformatics |
GenSel | 4.90 | [268] | Biology, Genetics |
GET_HOMOLOGUES | 20150529 | [269] | Biology, Genomics |
GFOLD | 1.1.4 | [270] | Biology, RNA-seq |
Gffread | 0.9.8c | [271] | Biology, Bioinformatics |
GKNO | 1.30.18 | [272] | Biology, NGS, |
Git | 1.8.2.1, 1.9.0 | [273] | Development, Revision Control |
Glimmer | 3.02 | [274] | Biology, Microbial Annotation |
Globus | 2.1.3 | [275] | Data Transfer |
GLPK | 4.55 | [276] | Biology, Genomics |
Gmap | 20150723, 20160501, 20160816 | [277] | Biology, Genomics |
GNU Compilers | 5.2.0 | [278] | Compilers, Programming |
GnuPlot | 4.6.0, 5.0.3 | [279] | Graphics, Plotting, Programming |
Grace | 5.1.22 | [280] | Graphics, plotting, 2D |
GrADS | 2.0.1 | [281] | Earth Science |
GramCluster | 1.3 | [282] | Biology, Sequencing |
GRASS | 7.0 | [283] | Geography |
GraphViz | 2.38.0 | [284] | Graphics, plotting, visualization |
GraphMap | 0.4.0 | [285] | Biology, Sequencing |
Gromacs | 4.5.5, 4.6.5, 5.1.2 | [286] | Chemistry, Modeling, Simulation |
GSNP | 1.0 | [287] | Biology, Bioinformatics, NGS |
GSL | 1.15 | [288] | Library, Math, C++, C |
Gsutil | 4.15 | [289] | Cloud, Storage, Google |
Gubbins | 20150519, 20160421 | [290] | Biology, Phylogenetics, Genomics |
GULP | 4.0 | [291] | Material Science |
HaMStR | 13.2.2, 13.2.3, 13.2.4 | [292] | Biology, Genomics |
HapCompass | 0.7.7 | [293] | Biology, NGS, Genomics |
HAPCUT | 0.7 | [294] | Biology, Assembly |
Hapsembler | 2.21 | [295] | Biology, Genomics, NGS |
HapTree | 1.0 | [296] | Biology, Genomics, NGS |
hapQTL | 1.00 | [297] | Biology, Genomics |
HDF4 | 4.2.11 | [298] | Library, Data |
HDF5 | 1.8.9, 1.8.12, 1.8.15 | [299] | Library, Data |
HGTFinder | 20160720 | [300] | Biology, Genomics |
HISAT2 | 2.0.0b, 2.0.1b, 2.0.3b | [301] | Biology, Sequence Alignment, NGS |
HMMER3 | 3.0, 3.1b1, 3.1b2 | [302] | Biology, Genomics |
HMMSplicer | 0.9.5 | [303] | Biology, Genomics |
HOMER | 4.2, 4.7, 4.8 | [304] | Biology, Genomics |
HOOMD | 1.3.3 | [305] | Chemistry |
HTMLDoc | 1.2.82 | [306] | Documentation, PDF, HTML |
HTSeq | 0.5.3p3, 0.6.1p1 | [307] | Biology, NGS |
Hyb | 20141126 | [308] | Biology, NGS, RNA-Seq |
HyPhy | 2.1.2.28, 2.2.6.1 | [309] | Biology, Phylogenetics |
Hypre | 1.10.0b, 2.8.0b | [310] | Library, Math, Physics |
iAssembler | 1.32 | [311] | Biology, Assembly |
IBDNe | 20150815 | [312] | Biology, NGS |
iCommands | 3.3.1 | [313] | Biology, iPlant, Data Tansfer |
ICORN2 | 0.95 | [314] | Biology, Sequencing |
IDBA-UD | 1.0.9, 1.1.0, 1.1.1 | [315] | Biology, NGS |
IDBA-MT | 1.0 | [316] | Biology, NGS |
IEP | 3.6 | [317] | Programming, Python, Editor |
IGB | 8.4.1 | [318] | Biology, Genomics, NGS |
IGV | 2.3.91 | [319] | Biology, Bioinformatics, NGS |
iGTP | 1.1 | [320] | Biology, Bioinformatics, Phylogenetics |
illumiprocessor | 20150803 | [321] | Biology, Sequencing |
IM and IMa | 20091217 | [322] | Biology, Population |
IMa2 | 20120827 | [323] | Biology, Population |
ImageJ | 1.48 | [324] | Image manipulation |
ImageMagick | 6.8.8-9 | [325] | Image manipulation |
IMOD | 4.7.15 | [326] | 3D modeling, Image Reconstruction |
InParanoid | 4.1 | [327] | Biology, Bioinformatics |
Intel Compilers | 2016.0.109 | [328] | Programming, Compilers |
IOAPI | 3.1 | [329] | Meteorology |
Iprscan | 4.8 | [330] | Biology, Genomics |
ipyrad | 0.4.4 | [331] | Biology, bioinformatics, NGS |
IQ-TREE | 1.4.0, 1.4.2, 1.5.3 | [332] | Biology, Phylogenetics |
IRAP | 0.8.1p7 | [333] | Biology, NGS, RNA-seq |
iRep | 20161015 | [334] | Biology, |
ITK | 4.3.1 | [335] | Biology, Genomics |
ITK-SNAP | 3.0.0 | [336] | Biology, Neuroscience, Imaging |
JAGS | 3.3.0 | [337] | Statistics |
Java | 1.7.0_79, 1.8.0_31 | [338] | Java Development Kit |
Je | 1.0. | [339] | Biology, NGS |
Jellyfish | 2.1.1 | [340] | Biology, NGS |
JModelTest | 2.1.1 | [341] | Biology, Phylogenetics, Genomics |
Julia | 0.3.11, 0.4.6 | [342] | Programming, Languages |
KaKs | 1.2 | [343] | Biology, Phylogenetics |
Kent | 20120524 | [344] | Biology, NGS |
Khmer | 1.1, 2.0 | [345] | Biology, NGS |
KIM | 1.7.2 | [346] | Library |
KING | 1.4, 1.9 | [347] | Biology, Genomics |
KisSplice | 2.4.0-p1 | [348] | Biology, NGS |
Kallisto | 0.42.3, 0.42.4 | [349] | Biology, NGS, RNA-Seq |
KERAS | 1.0.8 | [350] | Deep Learning |
Kmer | 1934 | [351] | Biology, NGS |
KmerGenie | 1.6741 | [352] | Biology, NGS, Utilities |
Kraken | 0.10.4b | [353] | Biology, Genomics, Phylogenetics |
Krona | 20161019 | [354] | Biology, Bioinformatics |
Lace | 0.99 | [355] | Biology, NGS |
LAMMPS | 28Oct12, 30Sep13, 28Jun14 | [356] | Molecular Dynamics Simulation |
LAMP | 2.5 | [357] | Biology, Genomics |
Last | 247, 531, 801 | [358] | Biology, Sequence alignment |
Lastz | 1.03.02, 1.02.00 | [359] | Biology, NGS |
LDhat | 2.2a | [360] | Biology, Genomics |
LIBSVM | 3.12 | [361] | Machine Learning |
LIGR | 2.05 | [362] | Biology, Assembly |
LINKS | 1.8.5 | [363] | Biology, Genomics |
LFMM | 1.4 | [364] | Biology, Genomics |
LSC | 0.3, 0.3.1 | [365] | Biology, NGS, Error correction |
lobSTR | 4.0.6 | [366] | Biology, Phylogenetics |
Loci | 3.3 | [367] | Fluid Dynamics |
LoRMA | 0.3 | [368] | Biology, NGS |
LS-DYNA | 700, 711, 800 | [369] | Physics |
Lumpy | 0.2.1 | [370] | Biology, SNP |
LZO | 2.09 | [371] | Library, Data Compression |
MACH | 1.0.18 | [372] | Biology, Genomics |
Mach2VCF | 20150515 | [373] | Biology |
M5tools | 20121126 | [374] | Biology, Bioinformatics, Genomics |
MACS | 1.4.2, 2.1.1 | [375] | Biology, ChIP-Seq |
mafft | 7.215, 7.245, 7.294 | [376] | Biology, Multiple sequence alignment |
Mash | 1.1 | [377] | Biology, Genomics |
Maker | 2.25b, 2.31.6, 2.31.8 | [378] | Biology, Annotation, Genomics |
MapSplice | 2.1.7 | [379] | Biology, NGS, RNA-Seq |
MAPminer | 1.1 | [380] | Biology, Phylogenetics |
MassMine | 0.9.5, 0.10.0, 0.11.0 | [381] | Data Mining |
Maq | 0.7.1 | [382] | Biology, NGS |
MARK | 2.0.1 | [383] | Statistics |
MarkerMiner | 20150429, 20150511 | [384] | Biology, Genomics |
MaSuRCA | 2.3.2, 3.2.1 | [385] | Biology, NGS |
Matlab | 2012a, 2013a, 2014a | [386] | Math, Simulation, Programming |
MATS | 2.1.0, 3.0.8, 3.0.9 | [387] | BIology, NGS |
Mauve | 2.3.1 | [388] | Biology, NGS |
MaxBin | 2.1.1 | [389] | Biology, NGS |
MCarts | 1.0.2 | [390] | Biology, Genomics, Markov models |
MCNP | 5, 6b2, 6, 6.1 | [391] | Physics |
MCNPX | 2.7.0, 2.7.0-i8 | [392] | Physics |
MEGAN | 5.10.3, 6.4.15 | [393] | Biology, NGS |
Megraft | 1.0.2 | [394] | Biology, Sequencing |
Melting | 4.3.1 | [395] | Biology, Genome, RNA, Folding |
Meme | 4.11.1, 4.11.2 | [396] | Biology, Motifs, Sequence analysis |
Meraculous | 2.0.5 | [397] | Biology, NGS |
Mercurial | 4.0.2 | [398] | Development, Revision Control |
Merlin | 1.1.2 | [399] | Biogolgy, SNP |
Meta-Tissue | 0.4 | [400] | Biology, Genetics |
Metabin | 1.0 | [401] | Biology, Metagenomics |
MetaCluster | 5.0b | [402] | Biology, Metagenomics |
MetaCV | 2.3.0 | [403] | Biology, NGS |
METAL | 20110325 | [404] | Biology, Genomics |
MetAMOS | 1.5.0rc4-20140827 | [405] | Biology, Bioinformatics, Genomics, Assembly |
Metassembler | 1.5 | [406] | Biology, Genomics |
MetaVelvet | 1.2.01 | [407] | Biology, NGS |
Metaxa2 | 2.0.2, 2.1.1 | [408] | Biology, NGS |
MetaGeneMark | 2012.04 | [409] | Biology, Genomics |
Mfold | 3.6 | [410] | Biology, Genomics |
MGEScan | 1.1 | [411] | Biology, Genomics |
MHAP | 1.6 | [412] | Biology, Sequencing |
MIA | 20130301 | [413] | Biology, NGS |
MicrobeCensus | 1.0.7 | [414] | Biology, NGS |
MIDAS | 20160830 | [415] | Biology, Phylogenetics |
Midnight Commander | 4.6.1 | [416] | Tools, Utilities |
Migrate-n | 3.3.0, 3.6.6, 3.6.11 | [417] | Biology, Population |
Minced | 0.2.0 | [418] | Biology, Genomics |
Minimac | 2-20140915, 3-20151015 | [419] | Biology, Genomics |
mira | 3.9.18, 4.0.rc1, 4.0.2 | [420] | Biology, NGS |
MISO | 0.4.9, 0.5.2, 0.5.3 | [421] | Biology, NGS |
MMSEQ | 1.0.8 | [422] | Biology, NGS |
MSMBuilder | 2.5.1 | [423] | Molecular Dynamics |
MOABS | 1.2.9, 1.3.2, 1.3.4 | [424] | Biology, NGS, Genomics |
Modeller | 9.11, 9.13, 9.14 | [425] | Biology, Modeling |
Molden | 5.0 | [426] | Molecular, electronic structure |
MolPro | 2012.1p22 | [427] | Quantum Chemistry, Ab Initio |
mosaik | 2.1.33, 2.2.3 | [428] | Biology,NGS |
Mothur | 1.36.1, 1.37.0, 1.38.1 | [429] | Biology, Microbial Ecology |
MotionCorr | 2.1 | [430] | Motion Correction |
MotionCor2 | 01302017 | [431] | Motion Correction |
MOTU | 1.1 | [432] | Biology, Bioinformatics, Genomics |
MPE2 | 2.4.9b | [433] | MPI |
MP-EST | 1.4, 1.5 | [434] | Biology, Phylogenetics |
mpiP | 3.4.1 | [435] | Parallel Computing |
MrBayes | 3.2.1, 3.2.4, 3.2.5 | [436] | Biology, Phylogenetics |
MRIcron | 201306 | [437] | Biology, MRI, Imaging |
MUMmer | 3.23 | [438] | Biology, Genomics |
MUSCLE | 3.8.31 | [439] | Biology, Genomics |
MuTect | 1.1.4, 1.1.7 | [440] | Biology, Genomics |
MutSig | 1.4, 1.41 | [441] | Biology, Genomics |
MZMine | 2.19, 2.20, 2.21 | [442] | Biology, Spectroscopy |
NAMD | 2.9, 2.11, 2.12 | [443] | Molecular Dynamics, Chemistry |
Nanocorrect | 20150727 | [444] | Biology, NGS |
Nanopolish | 20150904 | [445] | Biology |
Nbody | 6 | [446] | Astronomy |
NCBI C++ Toolkit | 12.0.0 | [447] | Biology, C++, Development |
NCL | 6.1.2, 6.3.0 | [448] | Atmosphere Science |
NCO | 4.2.1, 4.4.3 | [449] | Data exchange tools |
Ncview | 2.1.2 | [450] | Data visualization |
NeEstimator | 2.01 | [451] | Biology, Bioinformatics |
NetCDF | 3.4.2, 4.2, 4.3 | [452] | Data exchange, Tools |
NEURON | 7.4 | [453] | Biology, Neuroscience |
Newbler | 2.7, 2.8, 2.9 | [454] | Biology, NGS |
Newick utils | 1.6 | [455] | Biology, Phylogenetics |
Nextallele | 20140718 | [456] | Biology, Genomics |
NextGenMap | 0.5.3 | [457] | Biology, Bioinformatics, NGS |
Nexus NCL | 2.1.18 | [458] | Biology, Phylogenetics, Library |
NGS-bits | 0.1 | [459] | Biology, Sequencing |
ngsCAT | 0.1 | [460] | Biology, Bioinformatics, NGS |
ngsTools | 20150816 | [461] | Biology, NGS |
NGSUtils | 20130722, 20150206 | [462] | Biology, NGS |
Nipype | 0.10.0, 0.12.1 | [463] | Biology, Bioinformatics, Neuroscience, Imaging |
NMRPipe | 7.9 | [464] | Biology, Biochemistry |
Novoalign | 2.08.02, 3.00.02 | [465] | Biology, NGS |
NWChem | 6.5, 6.6 | [466] | Chemistry |
NxTrim | 0.4.1 | [467] | Biology, Bioinformatics, NGS |
Oases | 0.2.08 | [468] | Biology, NGS |
Olego | 1.1.2, 1.1.5, 1.1.6 | [469] | Biology, NGS, RNA-Seq |
OCaml | 4.02.3 | [470] | Programming Languages, Scripting, Development |
Octave | 3.6.4 | [471] | Numerical Computation |
Oncotator | 1.5.2.0, 1.5.3.0, 1.8.0.0 | [472] | Biology, Genomics |
OpenBabel | 2.3.2 | [473] | Biology, Chemistry |
OpenCL | 1.1 | [474] | Programming, Library |
OpenCV | 2.4.8 | [475] | Computervision |
OpenFOAM | 2.1.1, 3.0.1, 4.0 | [476] | Fluid Dynamics |
OpenMM | 6.2.0 | [477] | Quantum Chemistry |
Orange3 | 3.3.6 | [478] | Data Mining, Visualization |
OrthoFinder | 0.2.5, 0.6.0, 1.0.2 | [479] | Biology, Genomics |
OrthoMCL | 2.0.2, 2.0.3, 2.0.7 | [480] | Biology, Genomics |
OTB | 5.6.1 | [481] | Geospacial Imaging |
p4vasp | 0.3.29 | [482] | Molecular, Electronic Structure |
p53MH | 20020901 | [483] | Biology, Sequencing |
Pacbio | 2.2.0, 2.3.0p5 | [484] | Biology, Bioinformatics, NGS |
Package-GFE | 20150701 | [485] | Biology, Genomics |
PALES | 122 | [486] | Physics |
PALADIN | 1.3.1 | [487] | Biology, Phylogenetics |
PAML | 4.7, 4.8a, 4.9a | [488] | Biology, Phylogenetics |
Pandaseq | 20140808, 20150627 | [489] | Biology, Bioinformatics, NGS, Sequencing |
PAPI | 5.1.0.2 | [490] | Software, Computing |
Parallel | 20150122, 20170322 | [491] | Programming, Languages |
ParaView | 4.1.0, 4.2.0, 4.3.0 | [492] | Data Analysis |
Parsimonator | 1.0.2 | [493] | Biology, Bioinformatics |
PartitionFinder | 1.1.1, 2.1.1 | [494] | Biology, Phylogenetics, Evolution |
Parflow | v615 | [495] | Ecology, Modeling |
PASA | 1.5, 2.0-r20150209 | [496] | Biology, Genomics |
PASTA | 20160616 | [497] | Biology, Sequence alignment, |
PAUP | 4.0b10, 4.1a147, 4.0a152 | [498] | Biology, Phylogenetics |
PAUDA | 1.0.1 | [499] | Biology, Bioinformatics, Sequence alignment |
PBalign | 20160921 | [500] | Biology, Bioinformatics |
PBCore | 20151201 | [501] | Biology, Bioinformatics |
PBCommand | 20151203 | [502] | Biology, Library |
PBJelly | 14.7.14, 15.2.20, 15.8.24 | [503] | Biology, Bioinformatics |
pbsdrmaa | 1.0.17 | [504] | Libraries, Torque |
p4est | 1.1 | [505] | Library |
pbsmrtpipe | 20151202 | [506] | Biology |
PeakSplitter | 1.0 | [507] | Biology, Chip-Seq |
PEAR | 0.9.2, 0.9.6 | [508] | Biology, NGS |
PDT | 3.18, 3.20, 3.22 | [509] | Programming, Profiler |
Perl | 5.16.0 | [510] | Programming, Language |
PerM | 0.4.0 | [511] | Biology, NGS |
PETSc | 2.3, 3.3 | [512] | Math, Numerical solvers |
PGDSpider | 2.0.9.0 | [513] | Biology, NGS |
PHAST | 1.4 | [514] | Biology, Phylogenetics |
Phenix | 1.8.1069, 1.10.2155 | [515] | Crystallography |
PHYLDOG | 20130418 | [516] | Biology, Genomics, Phylogenetics |
Phyluce | 20140427, 20151103, 20160715 | [517] | Biology, Phylogenetics |
Phyutility | 2.7.1 | [518] | Biology, Bioinformatics |
PfamScan | 1.3 | [519] | Biology, Genomics |
PHITS | 2.52, 2.76. 2.82 | [520] | Physics |
PIPE-CLIP | 1.1.0 | [521] | Biology, NGS |
Pipits | 1.3.6 | [522] | Biology, Sequencing |
piPipes | 1.5.0 | [523] | Biology, Phylogenetics |
Phonopy | 1.9.2 | [524] | Chemistry |
PHYLIP | 3.696 | [525] | Biology, Phylogenetics |
PhyloBayes | 3.3f, 1.4f MPI | [526] | Biology, Phylogenetics |
PhyloNet | 3.5.7 | [527] | Biology, Phylogenetics |
Phylosift | 1.1 | [528] | Biology, Genomics, Phylogenetics, Taxonomy |
PhyML | 3.0, 3.1 | [529] | Biology, Phylogenetics |
Picard | 1.72, 1.80, 2.0.1 | [530] | Biology, NGS |
PICRUSt | 1.0.0, 1.1.0 | [531] | Biology, Phylogenetics |
Pilon | 1.22 | [532] | Biology, Bioinformatics |
Piranha | 1.2.1 | [533] | Biology, Phylogenetics |
PLAST | 1.0 | [534] | Biology, Bioinformatics |
Platypus | 0.8.1 | [535] | Biology, NGS |
Plink | 1.07, 1.90b3, 1.90b3.39 | [536] | Biology, GWAS |
PLINKSEQ | 0.10 | [537] | Biology, Genomics |
PluMiST | 1.1 | [538] | Biology, Phylogenetics, Genomics |
PolyPhen | 2.2.2.r405b | [539] | Biology, Genomics |
PonyTools | 0.1 | [540] | Biology, Genomics |
Poretools | 0.5.0 | [541] | Biology, Sequencing |
POV-Ray | 3.7 | [542] | 3D, Graphics |
Prank | 20150803 | [543] | Biology, Bioinformatics, Alignment |
Preseq | 0.0.4 | [544] | Biology, NGS |
PRICE | 1.2 | [545] | Biology, NGS |
Primer3 | 2.3.4 | [546] | Biology, Genomics |
PRIMUS | 1.8.0 | [547] | Biology, Phylogenetics |
PRINSEQ | 0.20.4 | [548] | Biology, Sequencing |
Prodigal | 2.6.3 | [549] | Biology, Genomics |
ProfessAtQE | 2014 | [550] | Material Science, Molecular Dynamics |
Prokka | 1.10, 1.11 | [551] | Biology, Genomics, Bioinformatics, Assembly |
ProBABEL | 0.4.2, 0.4.3, 0.4.5 | [552] | Biology, Genomics, GWAS |
Probalign | 1.4 | [553] | Biology, Genomics |
Proovread | 1.03rcl | [554] | Biology, Genomics, NGS |
Proteinortho | 4.26, 5.11 | [555] | Biology, Genomics |
PROVEAN | 1.1.5 | [556] | Biology, Genomics |
PyAni | 0.2.1 | [557] | Bilogy, Genomics |
PyHDF | 0.9.0 | [558] | Library, HDF4 |
PyVCF | 0.6.0 | [559] | Biology |
Python | 2.7.6, 3.5.0 | [560] | Biology, Genomics, NGS |
Pyfasta | 0.5.2 | [561] | Biology, Phylogenetics |
Pyrad | 3.0.63 | [562] | Biology, Sequencing Alignment, Assembly |
QDD | 3.1.2 | [563] | Programming, scripting, language |
QGIS | 2.18.0 | [564] | Geography |
QIIME | 1.9.0, 1.9.1 | [565] | Biology, Ecology |
QIIME2 | 2.0.6 | [566] | Biology, Ecology |
QT | 4.8.3 | [567] | Computer Science |
QUAST | 2.3, 4.4 | [568] | Biology, NGS |
Quake | 0.3 | [569] | Biology, Sequencing |
Quantas | 1.0.4, 1.0.8 | [570] | Biology, Bioinformatics, NGS |
QualiMap | 2.1.1 | [571] | Biology, Sequence alignment |
Quickquartet | 1.0.0 | [572] | Biology, Phylogenetics |
R | Rmpi/3.3.1, 3.2.0, 3.3.0 | [573] | Statistics, Programming |
R2R | 1.0.4 | [574] | Biology, RNA |
R8S | 1.71, 1.8 | [575] | Biology, Evolution |
Racon | 20161013 | [576] | Biology, Sequencing |
RADICAL | 0.2 | [577] | Biology, Phylogenetics, Genomics |
Randfold | 2.0.1 | [578] | Biology, RNA |
Rascaf | 1.0.2 | [579] | Biology, RNA-Seq |
RAxML | 8.1.23, 8.2.2, 8.2.3 | [580] | Biology, Phylogenetics |
Ray | 2.3.1 | [581] | Biology, Genomics, NGS |
REAGO | 1.1 | [582] | Biology, Assembly |
REAPR | 1.0.18 | [583] | Biology, Bioinformatics, Assembly |
Recycler | 0.62 | [584] | Biology, Bioinformatics |
RELION | 1.4 | [585] | Biology, Bioinformatics |
REPdenovo | 20170222 | [586] | Biology, Phylogenetics |
RepeatExplorer | 20150506 | [587] | Biology, Genomics |
RepeatMasker | 3.3.0 | [588] | Biology, Genomics |
RepeatModeler | 1.0.8 | [589] | Biology, Bioinformatics |
Reptile | 1.1 | [590] | Biology, NGS, error correction |
RevBayes | 1.0.0, 1.0.3 | [591] | Biology, Phylogenetics |
riboPicker | 0.4.3 | [592] | Biology, Sequence |
RNAhybrid | 2.1.1 | [593] | Biology, Genomics |
rRNASelector | 1.0.0 | [594] | Biology, Sequencing |
rnaseqlib | 20150721 | [595] | Biology, Phylogenetics, RNA-Seq |
rnaQUAST | 1.2.0 | [596] | Biology, NGS, Sequencing |
ROOT | 6.0 | [597] | Data Analysis |
Roary | 3.4.1 | [598] | Biology, Genomics |
Rosetta | 2014wk4 | [599] | Biology, Structure, Modelling |
RSEG | 0.4.8 | [600] | Biology, NGS |
RSEM | 1.2.19, 1.2.28, 1.2.29 | [601] | Biology, NGS, RNA-Seq |
RSeQC | 2.3.7, 2.6.2 | [602] | Biology, NGS, RNA-Seq |
RStudio | 0.99.902, 0.99.903 | [603] | R, Statistics, Programming |
RTGTools | 3.7.1 | [604] | Biology, NGS |
Ruby | 1.9.3-p0 | [605] | Programming, Scripting, Language |
Sailfish | 0.6.3 | [606] | Biology, NGS, RNA-Seq |
Salmon | 0.6.0, 0.7.2 | [607] | Biology, RNA-seq |
SMC++ | 1.7.0 | [608] | Biology, NGS |
Sambamba | 0.5.0-dev, 0.5.10, 0.6.3 | [609] | Biology, NGS |
Samstat | 1.08 | [610] | Biology, NGS, Bioinformatics, Sequencing |
Samblaster | 0.1.14 | [611] | Biology, NGS |
samtools | 1.1, 1.2, 1.3.1 | [612] | Biology, NGS |
SAS | 9.3 | [613] | Statistics, Graphing |
SATe | 2.2.7 | [614] | Biology, Phylogenetics |
Scala | 2.11.5 | [615] | Programming, Language |
Scalablast | 2.4.53 | [616] | Biology, Genomics |
Scalpel | 0.1.1 | [617] | Biology, NGS |
SCRIPTURE | 20101211 | [618] | Biology, Bioinformatics, Genomics |
Shannon | 20160211 | [619] | Biology, RNA-Seq |
SHAPEIT | 2.5.5 | [620] | Biology, SNP |
SHAPE-MaP | 1.2 | [621] | Biology, Phylogenetics |
Sharcgs | 1.2.11 | [622] | Biology, NGS, Assembly |
SHEsisPlus | 1.0 | [623] | Biology, Phylogenetics |
shustring | 2.6 | [624] | Biology, Sequencing |
SCons | 2.3.0 | [625] | Programming |
Scoary | 1.6.10 | [626] | Biology, Bioinformatics, Genomics |
SCRATCH1D | 1.0 | [627] | Biology, Genomics |
Scythe | 0.991 | [628] | Biology, NGS |
SDT | 1.2 | [629] | Biology, Sequencing |
Segemehl | 0.1.9 | [630] | Biology, NGS, Mapper |
SEPP | 1.0, 3.0 | [631] | Biology, Phylogenetics, HMM |
SGA | 0.10.14 | [632] | Biology, Assembly |
Seq-Gen | 1.3.3 | [633] | Biology, Phylogenetics |
SeqPrep | 0.5 | [634] | Biology, NGS |
Seqmagick | 20150923 | [635] | Biology, Phylogenetics |
SeqMap | 1.0.13 | [636] | Biology, NGS |
Seqtk | 20140729 | [637] | Biology, NGS |
SEQuel | 1.0.1 | [638] | Biology, NGS |
SeqyClean | 1.8.10 | [639] | Biology, NGS, Bioinformatics |
ShoRAH | 20131204 | [640] | Biology, NGS, quality filter |
SHRiMP | 2.2.3 | [641] | Biology, NGS |
SICER | 1.1 | [642] | Biology, ChIP-Seq |
Sickle | 1.200, 1.33 | [643] | Biology, NGS, quality filter |
Siesta | 2.0.2,3.1 | [644] | Simulation, Physics, Ab Initio |
SIFT | 4.0.3b | [645] | Biology, Genomics |
SignalP | 4.1c | [646] | Biology, NGS |
Silo | 4.7 | [647] | Library, Data |
SIPeS | 2.0 | [648] | Biology, Bioinformatics, ChIP-Seq |
Slicer | 4.3.1 | [649] | Biology, Imaging |
SMALT | 0.7.6 | [650] | Biology, NGS |
Snap | 20100728, 0.15.4 | [651] | Biology, Genomics |
SNAPE-pooled | 20130407 | [652] | Biology, SNP |
SNeP | 1.1 | [653] | Biology, Phylogenics |
SnpEff | 4.1i, 4.2, 4.3 | [654] | Biology, NGS, Genomics |
SNPhylo | 20140701 | [655] | Bilogy, Phylogenetics |
SNP-sites | 2.0.3 | [656] | Biology, SNP |
Snippy | 20160419 | [657] | Biology, Phylogenetics |
SOAPdenovo | 1.05 | [658] | Biology, NGS |
SOAPdenovo-Trans | 1.01, 1.03 | [659] | Biology, NGS |
SOAPec | 2.03 | [660] | Biology, Phylogenetics |
SOAPsplice | 1.10 | [661] | Biology, NGS |
SortMeRNA | 2.1 | [662] | Biology, Sequencing, NGS |
SparCC | 201402 | [663] | Microbial Ecology |
Spades | 3.8.0, 3.9.0, 3.10.0 | [664] | Biology, NGS |
Spanki | 0.4.1, 0.4.3, 0.5.0 | [665] | Biology, NGS, RNA-Seq |
SPARTA+ | 2.60 | [666] | Chemistry |
Spidey | 20150922 | [667] | Biology, Genomics |
SPIMAP | 1.1 | [668] | Biology, Phylogenetics |
SpliceTrap | 0.90.5 | [669] | Biology, NGS, RNA-Seq |
SPM | 8 | [670] | Biology, Statistics, Neurology, Imaging |
Sputnik | 1.0 | [671] | Biology, Genomics |
SQLite | 3.8.8.2 | [672] | Database |
SQL_Developer | 4.1.2 | [673] | Programming, Oracle, Sql |
SRA | 2.1.10 | [674] | biology, NGS |
SSPACE | 2.0, 3.0 | [675] | Biology, NGS |
SST-Core | 6.0.0 | [676] | MPI |
SSR_pipeline | 0.951 | [677] | Bilogy, DNA Sequencing |
Stacks | 1.24, 1.35, 1.45 | [678] | Biology, Genomics, NGS |
Staden | 1.14.6 | [679] | Biology, Sequencing |
Stampy | 1.0.31 | [680] | Biology, Bioinformatics, Sequencing |
STAR | 2.4.0j, 2.5.1b | [681] | Biology, NGS, Alignment |
STAR-CCM+ | 8.06 | [682] | Mechanical Engineering |
Stata | 10.1, 13 | [683] | Statistics, Data analysis |
Stringtie | 1.0.0, 1.1.2, 1.2.1 | [684] | Biology, NGS, Alignment |
Structure | 2.3.3, 2.3.4 | [685] | Biology, Population |
Subread | 1.5.0-p1, 1.5.1 | [686] | Biology, Sequencing, SNP |
Supernova | 1.1.5 | [687]] | Biology, Phylogeneitcs, NGS |
SUNDIALS | 2.3.0, 2.5.0 | [688] | Numerical Solver |
SVDetect | 0.8b | [689] | Biology, NGS, SNP |
swak4Foam | 2.x | [690] | Fluid Dynamics |
swarm | 1.2.11 | [691] | Data Analysis |
SWEEP | 20160722 | [692] | Biology, SNP |
Swig | 2.0.9 | [693] | Programming, C, C++, Python |
SwitchSeq | 20140907 | [694] | Biology, NGS |
Syzygy | 1.2.7 | [695] | Biology, Genomics |
TetGen | 1.5.0 | [696] | Tetrahedral Meshes 3D |
tapir | 20160825 | [697] | Biology, Phylogenetics |
TAPIS | 1.2.1 | [698] | Biology, Sequencing |
TASSEL | 5.0, 5.2.29 | [699] | Biology, Genomics |
TAU | 2.21.4, 2.23, 2.24, 2.52 | [700] | Profiling, Tracing, Programming |
taxMap | 0.1 | [701] | Biology, Phylogenetics, Taxonomy |
TaxonDNA | 1.8 | [702] | Biology, Taxonomy |
T-Coffee | 9.03.r1318 | [703] | Biology, Genomics, Multiple Alignment |
TEToolkit | 1.5.1 | [704] | Biology, Bioinformatics, Sequencing |
TensorFlow | 0.10.0, 1.0.0 | [705] | Library, Math |
TESS | 2.3.1 | [706] | Biology, Genomics, Markov |
tgicl | 2.1 | [707] | Biology, sequencing, clustering |
Tmux | 2.0 | [708] | GNU, Terminal Multiplexer |
TomoPy | 0.0.3 | [709] | Biology, Neuroimaging |
Tophat | 1.4.1, 2.0.13, 2.1.0 | [710] | Biology, NGS |
Torch | 20160704, 20171102 | [711] | Lua |
Totalview | 8.12.0 | [712] | Computer Science |
TPP | 4.7.0 | [713] | Bioinformatics, MassSpec |
TrackTools | 2011 | [714] | Bioinformatics |
TrackVis | 0.5.2.2 | [715] | Biology, Spectroscopy |
Tracula | 5.3.2014_05_26 | [716] | Biology, Bioinformatics, Neuroscience, Imaging |
TraitRate | 1.1 | [717] | Biology, Evolution |
Trans-ABySS | 1.5.4 | [718] | Biology, Phylogenetics |
TransDecoder | 20140704, 2.0.1, 3.0.0 | [719] | Biology, NGS |
Transrate | 1.0.1 | [720] | Biology, Assembly |
TraCeR | 20160519 | [721] | Biology, Bioinformatics |
TreeCorr | 3.2.3 | [722] | Physics |
TreeFix | 1.1.7, 1.1.10 | [723] | Biology, Phylogenetics |
TreeMix | 1.12 | [724] | Biology, Phylogenetics |
TreePL | 20150305 | [725] | Biology, Phylogenetics |
TriMetAss | 1.1 | [726] | Biology, Bioinformatics, NGS |
TRF | 4.04 | [727] | Biology, Genomics |
Trilinos | 11.4.1, 11.8.1 | [728] | Math Algorithm |
trimAl | 1.2 | [729] | Biology, Genomics, Sequence Alignment |
Trim Galore | 0.2.8, 0.4.1, 0.4.4 | [730] | Biology, NGS |
Trimmomatic | 0.32, 0.33, 0.36 | [731] | Biology, NGS |
Trinity | r20160329-2.2.0, r20161120-2.3.2 | [732] | Biology, NGS, RNA-Seq |
Trinotate | 2.0.1, 3.0.1 | [733] | Biology |
TRNAscan-SE | 1.23 | [734] | Biology, NGS, Bioinformatics |
Twinscan | 4.1.2 | [735] | Biology, Genomics |
usearch | 7.0.1001-64, 8.0.1517, 9.2.64 | [736] | Biology, Sequence analysis |
UDUNITS | 2.2.17 | [737] | Library, Units, Programming |
UFITS | 0.7.2 | [738] | Biology, NGS |
UNAFold | 3.8 | [739] | Biology, Genome, RNA, Folding |
UProC | 1.2.0 | [740] | Biology, Genomics |
Valgrind | 3.9.0 | [741] | Computer Science |
VarDictJava | 20160521 | [742] | Biology, NGS |
VarScan | 2.3.6 | [743] | Biology, NGS, Genomics |
VASP | 5.3.2, 5.3.3, 5.3.5, 5.4.1 | [744] | Quantum Chemistry, Ab Initio |
VAST-TOOLS | 20150506 | [745] | Biology, NGS, RNA-Seq |
VCFLib | 20141119, 20150313 | [746] | Biology, NGS, Genomics |
VCFtools | 0.1.12a, 0.1.12b, 0.1.14 | [747] | Biology, SNPs |
velvet | 1.2.06, 1.2.07, 1.2.10 | [748] | Biology, Genomics, NGS |
VEP | 74, 83 | [749] | Biology, NGS |
VICUNA | 1.3 | [750] | Biology, Assembly |
ViennaRNA | 2.2.6 | [751] | Biology, RNA-seq |
Vim | 7.4.5 | [752] | Programming, Scripting, Language |
vmd | 1.9.1 | [753] | Biology, Visualization |
VSearch | 20151022, 20161209-2.3.4 | [754] | Biology, NGS |
VT | 20140903, 20160129 | [755] | Biology, Genomics |
VTK | 6.1.0 | [756] | Visualization, Graphics |
V-Phaser2 | 02112013 | [757] | Biology, Phylogenetics |
Virsorter | 1.0.3 | [758] | Biology, Phylogenetics |
w2rap-contiger | 20161124 | [759] | Biology, Genomics |
Wannier90 | 1.2, 2.0.0 | [760] | Computational Physics |
WebLogo | 3.3, 3.5.0 | [761] | Biology, Genomics |
WEVOTE | 1.5.0, 1.8.0 | [762] | Biology, Genomics |
WDSSII | 1 | [763] | Meteorology |
WIEN2k | 12.1 | [764] | Material Science, Chemistry |
Wgs or Celera | 8.2, 8.3rc1, 8.3rc1.r4638 | [765] | Biology, NGS |
wublast | 2.0 | [766] | Biology, Sequence Alignment |
YAHA | 0.1.82 | [767] | Biology NGS |
Xander | 20151222 | [768] | Biology, Phylogenetics |
XCrySDen | 1.5.60 | [769] | Computational Material Science |
Yambo | 3.3.0 | [770] | Physics |
YASM | 1.3.0 | [771] | Computer Science |
Yasra | 2.32 | [772] | Biology, NGS |
Zagros | 1.0.0 | [773] | Biology, NGS |
Zeo++ | 0.2.2 | [774] | Chemistry |
Zorro | 2.2 | [775] | 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.