Difference between revisions of "Installed Software"

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Line 93: Line 93:
 
| [[Beagle|BEAGLE]] || 3.2.2, 4.0 || [http://faculty.washington.edu/browning/beagle/beagle.html] || Biology, Genetics, Genotyping  
 
| [[Beagle|BEAGLE]] || 3.2.2, 4.0 || [http://faculty.washington.edu/browning/beagle/beagle.html] || Biology, Genetics, Genotyping  
 
|-
 
|-
−
| [[Beast|BEAST]] || 1.7.5, '''1.8.1''', 2.1.3 || [http://www.beast2.org/wiki/index.php/Main_Page]|| Biology, Phylogenetics
+
| [[Beast|BEAST]] || 1.7.5, '''1.8.1''', 2.3.2 || [http://www.beast2.org/wiki/index.php/Main_Page]|| Biology, Phylogenetics
 
|-
 
|-
 
| [[Bedops]] || 2.4.2 || [http://www.uwencode.org/software]||  Biology, Bioinformatics, Sequence, NGS
 
| [[Bedops]] || 2.4.2 || [http://www.uwencode.org/software]||  Biology, Bioinformatics, Sequence, NGS

Revision as of 20:32, 10 January 2016

  • Last updated on 2016-01-10.
  • 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 1.3.4, 1.3.7, 1.5.2 [3] Biology, NGS
AdmixTools 20150311 [4] Biology, Bioinformatics, Genomics, NGS
ADMIXTURE 1.23 [5] Biology, Bioinformatics, Genomics, NGS
AEGeAn 0.14.0 [6] Biology, Genomics
AFNI 2013_05_31, 2013_11_24 [7] Biology, Statistics, Imaging, Neurology
Agalma 0.2.1, 0.3.5, 0.5.0 [8] Biology, Bioinformatics, Genomics, SNP
ALE 20150507 [9] Biology, Bioinformatics, Assembly
ALLPATHS-LG 42316, 44837 [10] Biology, NGS
Amber 11, 12, 14 [11] Simulation, chemistry
AMOS 3.1.0 [12] Biology, Genomics, NGS
ANNOVAR 20120621, 20150322 [13] Biology, Genomics
AStalavista 3.2 [14] Biology, NGS, RNA-Seq, Genomics
ASTRID 20150807 [15] Biology, Genomics
Atlas 3.10.1, 3.11.17 [16] Library, Math
Amuse 6.0, 10.0 [17] Astrophysics
ANGSD 20150306, 20150909 [18] Biology, NGS
Affymetrix Power Tools 1.15.0, 1.18.0 [19] Biology, Genomics, Microarray
ARC 20140312 [20] Biology, NGS
Armadillo 6.200.3 [21] Library, C++ , Math
Astral 4.7.6, 4.7.8, 4.7.9 [22] Biology, Bioinformatics, NGS, Phylogenetics
AtomEye 3 [23] Material Science
ATRAM 20140624 [24] Biology, NGS
Augustus 2.6, 3.2.1 [25] Biology, NGS
Auto3DEM 4.05.1 [26] Image Reconstruction
BamBam 1.0 [27] Biology, NGS
Bam-readcount 20150216 [28] Biology, NGS
Bamstats 20140602 [29] Biology, NGS
Bamtools 2.1.1 [30] Biology, NGS
BamUtil 1.0.2 [31] Biology, NGS
Bam-Readcount 20150616 [32]] Biology, Genomics
BAPS 6.0 [33] Biology, Populaton genetics
Basemount 0.1.2.464 [34] Biology, DNA Sequencing
BayesRate 1.3.43 [35] Biology, Phylogenetics
Bbcp 12.08.17.00.0 [36] Network file transfer
Bcbio-nextgen 0.8.7 [37] Biology, NGS
Bcftools 1.0, 1.2 [38] Biology, Genomics, NGS
Bcl2fastq 2.16 [39] Biology, NGS, Illumina
BEAGLE 3.2.2, 4.0 [40] Biology, Genetics, Genotyping
BEAST 1.7.5, 1.8.1, 2.3.2 [41] Biology, Phylogenetics
Bedops 2.4.2 [42] Biology, Bioinformatics, Sequence, NGS
BEDTools 2.17.0, 2.23.0, 2.24.0 [43] Biology, NGS
BEST 2.3 [44] Biology, Phylogenetics
BETA 1.0.5 [45] Biology, NGS
BFAST 0.7.0 [46] Biology, NGS
Bismark 0.7.4, 0.7.7, 0.13.0 [47] Biology, NGS, Methylation
Bioconductor Latest [48] Biology, R, Statistics
BioPerl 1.006901 [49] Biology, Perl
BioPython 1.59 [50] Biology, Python
BLASR 20130815 [51] Biology, NGS
NCBI BLAST 2.2.27, 2.2.28, 2.2.29 [52] Biology, Sequence alignment
Blast2go 2.5.0-20120705 [53] Biology, Annotation
BLAT 20120524 [54] Biology, Sequence alignment
Blender 2.63 [55] Graphics
Boost 1.49.0, 1.53.0, 1.54.0 [56] C++, Library
Bowtie 0.12.9, 1.0.0, 1.1.1 [57] Biology, NGS
Bowtie2 2.2.4, 2.2.5, 2.2.6 [58] Biology, NGS
BPP 1.9.0, 2.2, 3.2 [59] Biology, Phylogenetics
BRANCH 1.8.1 [60] Biology, NGS, Mapping
BRATNextGen 20150505 [61] Biology, Genomics
Bsmap 2.74, 2.87 [62] Biology, NGS, Methylation
Busco 1.1b1 [63] Biology, Genomics
Bwa 0.6.1, 0.7.11, 0.7.12 [64] Biology, NGS
Camino 20140723 [65] Biology, Neuroscience, Imaging
CAP3 20120705 [66] Biology, sequence assembly
CASAVA 1.8.2 [67] Biology, NGS
CD-HIT 4.6, 4.6.4 [68] Biology, Genomics
CDO 1.6.1 [69] Climate
CEAS 1.0.2 [70] Biology, Genomics
CellProfiler 2.0 [71] Biology, Image Analysis
CFITSIO 3.370 [72] Library, C
CGATools 1.6.0.42 [73] Biology, NGS
Charmm 36a3 [74] Simulation, Chemistry
Chartdirector 5.1.0 [75] Graphics
CheckM 1.0.4 [76] Biology, Genomics
Chimera 1.7 [77] Biology, Modeling
ChromEvol 2.0 [78] Biology, Phylogenetics
CIMS 4.1.2 [79] Biology, Genomics
Circos 0.63-pre11 [80] Biology, Visualization
CisGenome 2.0 [81] Biology, Genomics, Peak Calling
Clann 3.2.3 [82] Biology, Phylogenetics
CLARK 1.2.2-b [83] Biology, Genomics
CLHEP 2.2.0.1 [84] High Energy Physics
ClonalFrame 1.1, 1.2 [85] Biology, Genomics, NGS
ClonalFrameML 1.25 [86] Biology, Genomics, NGS
ClustalW 2.1 [87] Biology, Genomics
Cluster3 1.52 [88] Biology, Genomics
Clview 20130402 [89] Biology, Genomics
ClustalO 1.2.0 [90] Biology, Genomics
CMake 2.8.8, 2.9.12.1, 3.1.0 [91] Programming, Build System
CMWP 140518 [92] Biology, Genomics
CNVSeq 20110715 [93] Biology, NGS
Cobrapy 0.3.2 [94] Biology, Metabolomics, Modeling
Coevol 1.3c, 1.4b [95] Biology, Phylogenetics
CoMap 1.4.1 [96] Biology, Genomics
CONCOCT 0.3.1 [97] Biology, Genomics
CoNIFER 0.2.2 [98] Biology, Genomics
Consed 23.0 [99] Biology, Genomics
Coreutils 8.23 [100] GNU Utilities, Computer Science
covNMR 2014 [101] Biochemistry
CPLEX 12.6.5 [102] Optimizer
CUDA 4.2, 5.5 [103] Programming, Graphics
Crux 1.40 [104] Biology, Mass-Spectrometry
Cufflinks 1.3.0, 2.0.2, 2.2.1 [105] Biology, NGS
Cutadapt 1.1, 1.7.1, 1.8.1 [106] Biology, NGS
DAKOTA 5.4.0 [107] Computational Science
DaPars 0.9.0 [108] Biology, NGS, RNA-Seq
DCMTK 3.6.0 [109] Biology, Neuroscience, Imaging
DSSAT 4.5 [110] Biology
DDSCAT 7.3.0 [111] Astrophysics
DDT 4.1.0, 4.2.1 [112] Software
Dealii 8.3.0 [113] Library
Delft3D 3621 [114] Hydrodynamics, Physics
Desmond 3.0.3.1 [115] Simulation, Biology, Chemistry
DETONATE 1.9 [116] Biology, NGS
Dalton 2011 [117] Quantum Chemistry
Diamond 0.5.1 [118] Computational Biology, Genomics
Dibig Tools 1.0 [119] Bioinformatics, PBS, Torque, Jobs
DiffReps 1.55.4 [120] Biology, NGS, ChIP-Seq
Dindel 1.01 [121] Biology, NGS
DISCOVARdenovo 52488 [122] Biology, NGS
DIYABC 1.0.4.43b, 2.0.3 [123] Biology, Genomics
Dlpoly 4.03.4 [124] Simulation, Biology, Chemistry
Dlpoly-Classic 1.9 [125] Simulation, Biology, Chemistry
DNA Clust 3.0 [126] Biology, Genomics
Dock 6.5, 6.6, 6.7 [127] Chemistry, ligand binding prediction
DOT 2.0 [128] Biology, Bioinformatics, Docking
Doxygen 1.8.3.1 [129] Programming, Documentation
DSSP 2.2.1 [130] Biology, Molecular Dynamics
DTI-TK 2.3.1 [131] Biology, Neurology, Imaging
EA-Utils 1.1.2.537 [132] Biology, NGS
ECTools 20140311, 20141201 [133] Biology, Sequencing, Bioinformatics
EEGLAB 12.0.2.1b, 13.2.2b, 13.4.4b [134] Biology, Matlab
EIGENSOFT 4.2, 5.0.1, 6.0.1 [135] Biology, Population
emboss 6.5.7 [136] Biology, multi-tool suite
EMAN2 2.11 [137] Biology
EMIRGE 20130727 [138] Biology, NGS
Ensembl_Tools 80 [139] Biology, Bioinformatics
EPACTS 3.2.6 [140] Biology, Bioinformatics, Genomics
EPOCH 4.7.3 [141] Astronomy, CPPP
eQTLA 1.1 [142] Biology, Genomics
Eqtlbma 1.2.2 [143] Biology, Genotyping
Esmf 6.3.0rp1 [144] Climate
Espresso 5.0.1, 5.2.0, 5.2.1 [145] Modeling, Physics
ESPRIT 201211 [146] Biology, NGS, Metagenomics
ETE2 2.1 [147] Biology, Phylogenetics
Eval 2.2.8 [148] Biology, Genomics, GUI
ExaBayes 1.2.1, 1.4.1 [149] Biology, Phylogenetics
ExaML 1.0.5, 1.0.12, 3.0.14 [150] Biology, Phylogenetics
ExomeCNV 1.4 [151] Biology, NGS, Genomics
Exonerate 2.2.0 [152] Biology, Genomics
eXpress 1.3.1 [153] Biology, NGS
FAR 2.15 [154] Biology, Genomics
FASTA 34.26.5, 36.3.6d [155] Biology, Genomics
FastML 3.0 [156] Biology, Phylogenetics, ML
FastQC 0.9.6, 0.10.1 [157] Biology, NGS
Fastq-tools 0.7, 0.8 [158] Biology, NGS
FastStructure 20150112 [159] Biology, Genomics
FastTree 2.1.7 [160] Biology, Phylogenetics
Fastx_toolkit 0.0.13.2 [161] Biology, NGS
Fathmm 20150225 [162] Biology, Genomics
fcGENE 1.0.7 [163] Biology, Genomics, SNP
Ferret 6.82 [164] Oceanography, Meteorology
FFmpeg 2.1.3, 2.8.3 [165] Multimedia, audio, video
FFTW 3.3.2, 3.3.3 [166] Math, Library, C++
FLASH 1.2.10, 1.2.11 [167] Biology, Genomics, NGS
Flexbar 2.3 [168] Biology, Genomics, NGS
Fluent 14.5.7, 15.0.7, 16.0 [169] Simulation, Fluid Dynamics
FragGeneScan 1.16 [170] Biology, NGS, Genomics
FreeBayes 0.9.15, 0.9.21, 1.0.1 [171] Biology, NGS, SNP Calling
Freesurfer 5.2.0, 5.3.0 [172] Biology, Neurology, Imaging
FSL 5.0.2.2 [173] Biology, Neurology, Imaging
Galaxy latest [174] Biology, Chemistry, Other
GapFiller 1.11 [175] Biology, NGS
Garli 2.0, 2.01 [176] Biology, Phylogenetics
GAML 20150610 [177] Biology, NGS
GARM 0.7.4 [178] Biology, NGS
GASVPro 201310 [179] Biology, NGS, Genomics
GATE 7.0 [180] Data Analysis
GATK 1.6.9, 3.4.46, 3.5.0 [181] Biology, NGS
Gaussian G03, G09-A.02, G09-C.01 [182] Modeling, Computational Chemistry
Gblocks 0.91b [183] Genomics, Alignment tool
GCTA 1.24.7 [184] Biology, Genomics, SNP
GDAL 1.11.2 [185] Geospatial Data Modeling, Geospatial Library
Geant4 4.10 [186] Physics
GEM 20130406 [187] Biology, NGS
GEMINI 4.6.6a, 0.13.1 [188] Biology, Genomics, Genetics
GenBank Tools 20140130 [189] BIology< Genomics
GeneMark 2012.04 [190] Biology, Genomics, Metagenomics
GeneSeqer 20140226 [191] Biology, Genomics
Genewise 2.2.0 [192] Biology, Genomics, Annotation
Genome STRiP 2.00.1602 [193] Biology, genomics, NGS
GenomicTools 2.7.0 [194] Biology, NGS
GenomeTools 1.5.7 [195] Biology, Bioinformatics
GenSel 4.90 [196] Biology, Genetics
GET_HOMOLOGUES 20150529 [197] Biology, Genomics
GKNO 1.30.18 [198] Biology, NGS,
Git 1.8.2.1, 1.9.0 [199] Development, Revision Control
Globus 2.1.3 [200] Data Transfer
GLPK 4.55 [201] Biology, Genomics
Gmap 20150612, 20150723 [202] Biology, Genomics
GNU 4.4.6, 4.7.2 [203] Compilers, Programming
GnuPlot 4.6.0 [204] Graphics, Plotting, Programming
Grace 5.1.22 [205] Graphics, plotting, 2D
GrADS 2.0.1 [206] Earth Science
GramCluster 1.3 [207] Biology, Sequencing
GraphViz 2.38.0 [208] Graphics, plotting, visualization
Gromacs 4.5.5, 4.6.5 [209] Chemistry, Modeling, Simulation
GSNP 1.0 [210] Biology, Bioinformatics, NGS
GSL 1.15 [211] Library, Math, C++, C
Gsutil 4.15 [212] Cloud, Storage, Google
Gubbins 20150519 [213] Biology, Phylogenetics, Genomics
GULP 4.0 [214] Material Science
HaMStR 13.2.2, 13.2.3, 13.2.4 [215] Biology, Genomics
HapCompass 0.7.7 [216] Biology, NGS, Genomics
Hapsembler 2.21 [217] Biology, Genomics, NGS
HapTree 1.0 [218] Biology, Genomics, NGS
HDF4 4.2.11 [219] Library, Data
HDF5 1.8.9, 1.8.12, 1.8.15 [220] Library, Data
HISAT2 2.0.0b, 2.0.1b [221] Biology, Sequence Alignment, NGS
HMMER3 3.0, 3.1b1, 3.1b2 [222] Biology, Genomics
HMMSplicer 0.9.5 [223] Biology, Genomics
HOMER 4.2 [224] Biology, Genomics
HTMLDoc 1.2.82 [225] Documentation, PDF, HTML
HTSeq 0.5.3p3, 0.6.1p1 [226] Biology, NGS
Hyb 20141126 [227] Biology, NGS, RNA-Seq
HyPhy 2.1.2.28 [228] Biology, Phylogenetics
Hypre 1.10.0b, 2.8.0b [229] Library, Math, Physics
IBDNe 20150815 [230] Biology, NGS
IDBA-UD 1.0.9, 1.1.0, 1.1.1 [231] Biology, NGS
IDBA-MT 1.0 [232] Biology, NGS
IEP 3.6 [233] Programming, Python, Editor
IGB 8.4.1 [234] Biology, Genomics, NGS
iGTP 1.1 [235] Biology, Bioinformatics, Phylogenetics
illumiprocessor 20150803 [236] Biology, Sequencing
IM and IMa 20091217 [237] Biology, Population
IMa2 20120827 [238] Biology, Population
ImageJ 1.48 [239] Image manipulation
ImageMagick 6.8.8-9 [240] Image manipulation
Intel Compilers 11.1, 2012 [241] Programming, Compilers
IOAPI 3.1 [242] Meteorology
Iprscan 4.8 [243] Biology, Genomics
IQ-TREE 1.3.9, 1.3.10, 1.3.11 [244] Biology, Phylogenetics
ITK 4.3.1 [245] Biology, Genomics
ITK-SNAP 3.0.0 [246] Biology, Neuroscience, Imaging
JAGS 3.3.0 [247] Statistics
Java 1.6.0_31, 1.7.0_02, 1.8.0_31 [248] Java Development Kit
Jellyfish 2.1.1 [249] Biology, NGS
JModelTest 2.1.1 [250] Biology, Phylogenetics, Genomics
Julia 0.3.11 [251] Programming, Languages
KaKs 1.2 [252] Biology, Phylogenetics
Kent 20120524 [253] Biology, NGS
Khmer 1.1, 2.0 [254] Biology, NGS
KING 1.4 [255] Biology, Genomics
Kallisto 0.42.3, 0.42.4 [256] Biology, NGS, RNA-Seq
Kmer 1934 [257] Biology, NGS
KmerGenie 1.6741 [258] Biology, NGS, Utilities
Kraken 0.10.4b [259] Biology, Genomics, Phylogenetics
LAMMPS 28Oct12, 30Sep13, 28Jun14,15May15 [260] Molecular Dynamics Simulation
LAMP 2.5 [261] Biology, Genomics
Last 193, 247 [262] Biology, Sequence alignment
Lastz 1.03.02, 1.02.00 [263] Biology, NGS
LDhat 2.2a [264] Biology, Genomics
LIBSVM 3.12 [265] Machine Learning
LIGR 2.05 [266] Biology, Assembly
LSC 0.3, 0.3.1 [267] Biology, NGS, Error correction
Loci 3.3 [268] Fluid Dynamics
LS-DYNA 700, 711, 800 [269] Physics
Lumpy 0.2.1 [270] Biology, SNP
LZO 2.09 [271] Library, Data Compression
MACH 1.0.18 [272] Biology, Genomics
Mach2VCF 20150515 [273] Biology
M5tools 20121126 [274] Biology, Bioinformatics, Genomics
MACS 1.4.2 [275] Biology, ChIP-Seq
mafft 6.903, 7.215, 7.245 [276] Biology, Multiple sequence alignment
Maker 2.25b, 2.31.6, 2.31.8 [277] Biology, Annotation, Genomics
MapSplice 2.1.7 [278] Biology, NGS, RNA-Seq
MAPminer 1.1 [279] Biology, Phylogenetics
MassMine 0.9.5, 0.10.0 [280] Data Mining
Maq 0.7.1 [281] Biology, NGS
MARK 2.0.1 [282] Statistics
MarkerMiner 20150429, 20150511 [283] Biology, Genomics
MaSuRCA 2.3.2 [284] Biology, NGS
Matlab 2012a, 2013a, 2014a [285] Math, Simulation, Programming
MATS 2.1.0, 3.0.8, 3.0.9 [286] BIology, NGS
Mauve 2.3.1 [287] Biology, NGS
MaxBin 2.1.1 [288] Biology, NGS
MCarts 1.0.2 [289] Biology, Genomics, Markov models
MCNP 5, 6b2 [290] Physics
MCNPX 2.7.0, 2.7.0-i8 [291] Physics
MEGAN 5.10.3 [292] Biology, NGS
Megraft 1.0.2 [293] Biology, Sequencing
Melting 4.3.1 [294] Biology, Genome, RNA, Folding
Meme 4.8.1 [295] Biology, Motifs, Sequence analysis
Meraculous 2.0.5 [296] Biology, NGS
Mercurial 2.7 [297] Development, Revision Control
Merlin 1.1.2 [298] Biogolgy, SNP
Metabin 1.0 [299] Biology, Metagenomics
MetaCluster 5.0b [300] Biology, Metagenomics
MetaCV 2.3.0 [301] Biology, NGS
METAL 20110325 [302] Biology, Genomics
MetAMOS 1.5.0rc4-20140827 [303] Biology, Bioinformatics, Genomics, Assembly
Metassembler 1.5 [304] Biology, Genomics
MetaVelvet 1.2.01 [305] Biology, NGS
Metaxa2 2.0.2, 2.1.1 [306] Biology, NGS
MetaGeneMark 2012.04 [307] Biology, Genomics
Mfold 3.6 [308] Biology, Genomics
MHAP 1.6 [309] Biology, Sequencing
MIA 20130301 [310] Biology, NGS
Midnight Commander 4.6.1 [311] Tools, Utilities
Migrate-n 3.3.0, 3.6.6 [312] Biology, Population
Minimac 1-20130717, 2-20140915, 3-20150727 [313] Biology, Genomics
mira 3.9.18, 4.0.rc1, 4.0.2 [314] Biology, NGS
MISO 0.4.9, 0.5.2, 0.5.3 [315] Biology, NGS
MMSEQ 1.0.8 [316] Biology, NGS
MSMBuilder 2.5.1 [317] Molecular Dynamics
MOABS 1.2.9, 1.3.2, 1.3.4 [318] Biology, NGS, Genomics
Modeller 9.11, 9.13, 9.14 [319] Biology, Modeling
Molden 5.0 [320] Molecular, electronic structure
MolPro 2012.1p22 [321] Quantum Chemistry, Ab Initio
mosaik 2.1.33, 2.2.3 [322] Biology,NGS
Mothur 1.31.2, 1.36.1 [323] Biology, Microbial Ecology
MOTU 1.1 [324] Biology, Bioinformatics, Genomics
MP-EST 1.4 [325] Biology, Phylogenetics
mpiP 3.4.1 [326] Parallel Computing
MrBayes 3.2.1, 3.2.4, 3.2.5 [327] Biology, Phylogenetics
MRIcron 201306 [328] Biology, MRI, Imaging
MUMmer 3.23 [329] Biology, Genomics
MUSCLE 3.8.31 [330] Biology, Genomics
MuTect 1.1.4, 1.1.7 [331] Biology, Genomics
MutSig 1.4 [332] Biology, Genomics
MZMine 2.14.2, 2.15, 2.17 [333] Biology, Spectroscopy
NAMD 2.9 [334] Simulation, Chemistry, Biology
Nanocorrect 20150727 [335] Biology, NGS
Nanopolish 20150904 [336] Biology
Nbody 6 [337] Astronomy
NCBI C++ Toolkit 12.0.0 [338] Biology, C++, Development
NCL 6.1.2, 6.3.0 [339] Atmosphere Science
NCO 4.2.1, 4.4.3 [340] Data exchange tools
Ncview 2.1.2 [341] Data visualization
NetCDF 3.4.2, 4.2, 4.3 [342] Data exchange, Tools
Newbler 2.7, 2.8, 2.9 [343] Biology, NGS
Newick utils 1.6 [344] Biology, Phylogenetics
Nextallele 20140718 [345] Biology, Genomics
Nexus NCL 2.1.18 [346] Biology, Phylogenetics, Library
ngsCAT 0.1 [347] Biology, Bioinformatics, NGS
ngsTools 20150816 [348] Biology, NGS
NGSUtils 20130722, 20150206 [349] Biology, NGS
Nipype 0.10.0 [350] Biology, Bioinformatics, Neuroscience, Imaging
NMRPipe 7.9 [351] Biology, Biochemistry
Novoalign 2.08.02, 3.00.02 [352] Biology, NGS
NWChem 6.5 [353] Chemistry
Oases 0.2.08 [354] Biology, NGS
Olego 1.1.2, 1.1.5, 1.1.6 [355] Biology, NGS, RNA-Seq
OCaml 4.02.3 [356] Programming Languages, Scripting, Development
Octave 3.6.4 [357] Numerical Computation
Oncotator 1.5.2.0, 1.5.3.0, 1.8.0.0 [358] Biology, Genomics
OpenBabel 2.3.2 [359] Biology, Chemistry
OpenCL 1.1 [360] Programming, Library
OpenCV 2.4.8 [361] Computervision
OpenFOAM 2.1.1 [362] Fluid Dynamics
OpenMM 6.2.0 [363] Quantum Chemistry
OrthoFinder 0.2.5 [364] Biology, Genomics
OrthoMCL 2.0.2, 2.0.3, 2.0.7 [365] Biology, Genomics
p4vasp 0.3.29 [366] Molecular, Electronic Structure
Pacbio 2.2.0, 2.3.0 [367] Biology, Bioinformatics, NGS
Package-GFE 20150701 [368] Biology, Genomics
PALES 122 [369] Physics
PAML 4.7, 4.8a, 4.9a [370] Biology, Phylogenetics
Pandaseq 20140808, 20150627 [371] Biology, Bioinformatics, NGS, Sequencing
PAPI 5.1.0.2 [372] Software, Computing
Parallel 20150122 [373] Programming, Languages
ParaView 4.1.0, 4.2.0, 4.3.0 [374] Data Analysis
PartitionFinder 1.0.1, 1.1.1 [375] Biology, Phylogenetics, Evolution
Parflow v615 [376] Ecology, Modeling
PASA 1.5, 2.0-r20150209 [377] Biology, Genomics
PAUP 4.0b10 [378] Biology, Phylogenetics
PAUDA 1.0.1 [379] Biology, Bioinformatics, Sequence alignment
PBCore 20151201 [380] Biology, Bioinformatics
PBCommand 20151203 [381] Biology, Library
PBJelly 14.7.14, 15.2.20 [382] Biology, Bioinformatics
pbsdrmaa 1.0.17 [383] Libraries, Torque
p4est 1.1 [384] Library
pbsmrtpipe 20151202 [385] Biology
PeakSplitter 1.0 [386] Biology, Chip-Seq
PEAR 0.9.2, 0.9.6 [387] Biology, NGS
PDT 3.18 [388] Programming, Profiler
Perl 5.16.0 [389] Programming, Language
PerM 0.4.0 [390] Biology, NGS
PETSc 2.3, 3.3 [391] Math, Numerical solvers
PGDSpider 2.0.9.0 [392] Biology, NGS
Phenix 1.8.1069, 1.10.2155 [393] Crystallography
PHYLDOG 20130418 [394] Biology, Genomics, Phylogenetics
Phyluce 20140427, 20151103 [395] Biology, Phylogenetics
PfamScan 1.3 [396] Biology, Genomics
PHITS 2.52 [397] Physics
PIPE-CLIP 1.1.0 [398] Biology, NGS
Phonopy 1.9.2 [399] Chemistry
PHYLIP 3.696 [400] Biology, Phylogenetics
PhyloBayes 3.3f, 1.4f MPI [401] Biology, Phylogenetics
Phylosift 1.1 [402] Biology, Genomics, Phylogenetics, Taxonomy
PhyML 3.0, 20121109 [403] Biology, Phylogenetics
Picard 1.72, 1.80, 2.0.1 [404] Biology, NGS
PICRUSt 1.0.0 [405] Biology, Phylogenetics
Piranha 1.2.1 [406] Biology, Phylogenetics
PLAST 1.0 [407] Biology, Bioinformatics
Plink 1.07, 1.90b3 [408] Biology, GWAS
PLINKSEQ 0.10 [409] Biology, Genomics
PluMiST 1.1 [410] Biology, Phylogenetics, Genomics
PolyPhen 2.2.2.r405b [411] Biology, Genomics
Poretools 0.5.0 [412] Biology, Sequencing
POV-Ray 3.7 [413] 3D, Graphics
Preseq 0.0.4 [414] Biology, NGS
Primer3 2.3.4 [415] Biology, Genomics
ProfessAtQE 2014 [416] Material Science, Molecular Dynamics
Prokka 1.10, 1.11 [417] Biology, Genomics, Bioinformatics, Assembly
ProBABEL 0.4.2, 0.4.3, 0.4.5 [418] Biology, Genomics, GWAS
Probalign 1.4 [419] Biology, Genomics
Proovread 1.03rcl [420] Biology, Genomics, NGS
Proteinortho 4.26 [421] Biology, Genomics
PROVEAN 1.1.5 [422] Biology, Genomics
Python 2.7.6, 3.5.0 [423] Biology, Genomics, NGS
Pyrad 3.0.63 [424] Biology, Sequencing Alignment, Assembly
QDD 3.1.2 [425] Programming, scripting, language
QIIME 1.5.0 [426] Biology, Ecology
QT 4.8.3 [427] Computer Science
QUAST 2.3 [428] Biology, NGS
Quantas 1.0.4, 1.0.8 [429] Biology, Bioinformatics, NGS
QualiMap 2.1.1 [430] Biology, Sequence alignment
Quickquartet 1.0.0 [431] Biology, Phylogenetics
R Rmpi/2.15.1, 3.0.2, 3.2.0 [432] Statistics, Programming
R8S 1.71, 1.8 [433] Biology, Evolution
RADICAL 0.2 [434] Biology, Phylogenetics, Genomics
RAxML 8.1.23, 8.2.2, 8.2.3 [435] Biology, Phylogenetics
Ray 2.3.1 [436] Biology, Genomics, NGS
REAPR 1.0.18 [437] Biology, Bioinformatics, Assembly
RepeatExplorer 20150506 [438] Biology, Genomics
RepeatMasker 3.3.0 [439] Biology, Genomics
RepeatModeler 1.0.8 [440] Biology, Bioinformatics
Reptile 1.1 [441] Biology, NGS, error correction
riboPicker 0.4.3 [442] Biology, Sequence
RNAhybrid 2.1.1 [443] Biology, Genomics
ROOT 6.0 [444] Data Analysis
Roary 3.4.1 [445] Biology, Genomics
Rosetta 2014wk4 [446] Biology, Structure, Modelling
RSEG 0.4.8 [447] Biology, NGS
RSEM 1.1.17, 1.2.7, 1.2.19 [448] Biology, NGS, RNA-Seq
RSeQC 2.3.7, 2.6.2 [449] Biology, NGS, RNA-Seq
Ruby 1.9.3-p0 [450] Programming, Scripting, Language
Sailfish 0.6.3 [451] Biology, NGS, RNA-Seq
Sambamba 0.5.0-dev, 0.5.1 [452] Biology, NGS
Samstat 1.08 [453] Biology, NGS, Bioinformatics, Sequencing
Samblaster 0.1.14 [454] Biology, NGS
samtools 1.0, 1.1, 1.2 [455] Biology, NGS
SAS 9.3 [456] Statistics, Graphing
SATe 2.2.7 [457] Biology, Phylogenetics
Scala 2.11.5 [458] Programming, Language
Scalablast 2.4.53 [459] Biology, Genomics
Scalpel 0.1.1 [460] Biology, NGS
SHAPEIT 2.5.5 [461] Biology, SNP
Sharcgs 1.2.11 [462] Biology, NGS, Assembly
Schrodinger 2012, 2013 [463] Simulation, chemistry
SCons 2.3.0 [464] Programming
SCRATCH1D 1.0 [465] Biology, Genomics
Scythe 0.991 [466] Biology, NGS
Segemehl 0.1.9 [467] Biology, NGS, Mapper
SEPP 1.0, 3.0 [468] Biology, Phylogenetics, HMM
Seq-Gen 1.3.3 [469] Biology, Phylogenetics
SeqPrep 0.5 [470] Biology, NGS
SeqMap 1.0.13 [471] Biology, NGS
Seqtk 20140729 [472] Biology, NGS
SEQuel 1.0.1 [473] Biology, NGS
SeqyClean 1.8.10 [474] Biology, NGS, Bioinformatics
ShoRAH 20131204 [475] Biology, NGS, quality filter
SHRiMP 2.2.3 [476] Biology, NGS
Sickle 1.200, 1.33 [477] Biology, NGS, quality filter
Siesta 2.0.2,3.1 [478] Simulation, Physics, Ab Initio
SIFT 4.0.3b [479] Biology, Genomics
Silo 4.7 [480] Library, Data
SIPeS 2.0 [481] Biology, Bioinformatics, ChIP-Seq
Slicer 4.3.1 [482] Biology, Imaging
SMALT 0.7.6 [483] Biology, NGS
Snap 20100728 [484] Biology, Genomics
SNAPE-pooled 20130407 [485] Biology, SNP
SNeP 1.1 [486] Biology, Phylogenics
SnpEff 4.0e, 4.1i, 4.2 [487] Biology, NGS, Genomics
SNPhylo 20140701 [488] Bilogy, Phylogenetics
SOAPdenovo 1.05 [489] Biology, NGS
SOAPdenovo-Trans 1.01, 1.03 [490] Biology, NGS
SOAPsplice 1.10 [491] Biology, NGS
SparCC 201402 [492] Microbial Ecology
Spades 3.5.0, 3.6.0, 3.6.2 [493] Biology, NGS
Spanki 0.4.1, 0.4.3, 0.5.0 [494] Biology, NGS, RNA-Seq
SPARTA+ 2.60 [495] Chemistry
Spidey 20150922 [496] Biology, Genomics
SPIMAP 1.1 [497] Biology, Phylogenetics
SpliceTrap 0.90.5 [498] Biology, NGS, RNA-Seq
SPM 8 [499] Biology, Statistics, Neurology, Imaging
Sputnik 1.0 [500] Biology, Genomics
SQLite 3.8.8.2 [501] Database
SQL_Developer 4.1.2 [502] Programming, Oracle, Sql
SRA 2.1.10 [503] biology, NGS
SSPACE 2.0, 3.0 [504] Biology, NGS
Stacks 1.21, 1.24, 1.35 [505] Biology, Genomics, NGS
STAR 2.3.0e [506] Biology, NGS, Alignment
STAR-CCM+ 8.06 [507] Mechanical Engineering
Stata 10.1, 13 [508] Statistics, Data analysis
Stringtie 0.97, 1.0.0, 1.1.2 [509] Biology, NGS, Alignment
Structure 2.3.3, 2.3.4 [510] Biology, Population
SUNDIALS 2.3.0, 2.5.0 [511] Numerical Solver
SVDetect 0.8b [512] Biology, NGS, SNP
swak4Foam 2.x [513] Fluid Dynamics
swarm 1.2.11 [514] Data Analysis
Swig 2.0.9 [515] Programming, C, C++, Python
SwitchSeq 20140907 [516] Biology, NGS
Syzygy 1.2.7 [517] Biology, Genomics
TASSEL 5.0 [518] Biology, Genomics
TAU 2.21.4, 2.23 [519] Profiling, Tracing, Programming
T-Coffee 9.03.r1318 [520] Biology, Genomics, Multiple Alignment
TESS 2.3.1 [521] Biology, Genomics, Markov
tgicl 2.1 [522] Biology, sequencing, clustering
Tmux 2.0 [523] GNU, Terminal Multiplexer
TomoPy 0.0.3 [524] Biology, Neuroimaging
Tophat 1.4.1, 2.0.13, 2.1.0 [525] Biology, NGS
Torch 20151107 [526] Lua
Totalview 8.12.0 [527] Computer Science
TPP 4.7.0 [528] Bioinformatics, MassSpec
TrackTools 2011 [529] Bioinformatics
TrackVis 0.5.2.2 [530] Biology, Spectroscopy
Tracula 5.3.2014_05_26 [531] Biology, Bioinformatics, Neuroscience, Imaging
TraitRate 1.1 [532] Biology, Evolution
TransDecoder 20140704, 2.0.1 [533] Biology, NGS
Transrate 1.0.1 [534] Biology, Assembly
TreeFix 1.1.7, 1.1.10 [535] Biology, Phylogenetics
TreePL 20150305 [536] Biology, Phylogenetics
TriMetAss 1.1 [537] Biology, Bioinformatics, NGS
TRF 4.04 [538] Biology, Genomics
Trilinos 11.4.1, 11.8.1 [539] Math Algorithm
trimAl 1.2 [540] Biology, Genomics, Sequence Alignment
Trim Galore 0.2.8, 0.4.1 [541] Biology, NGS
Trimmomatic 0.22, 0.32, 0.33 [542] Biology, NGS
Trinity r20150302-2.0.6, r20151015-2.1.1 [543] Biology, NGS, RNA-Seq
Trinotate 2.0.1 [544] Biology
TRNAscan-SE 1.23 [545] Biology, NGS, Bioinformatics
Twinscan 4.1.2 [546] Biology, Genomics
usearch 7.0.1001-64, 8.0.1517 [547] Biology, Sequence analysis
UDUNITS 2.2.17 [548] Library, Units, Programming
UNAFold 3.8 [549] Biology, Genome, RNA, Folding
UProC 1.2.0 [550] Biology, Genomics
Valgrind 3.9.0 [551] Computer Science
VarScan 2.3.6 [552] Biology, NGS, Genomics
VASP 5.3.2, 5.3.3, 5.3.5 [553] Quantum Chemistry, Ab Initio
VAST-TOOLS 20150506 [554] Biology, NGS, RNA-Seq
VCFLib 20141119, 20150313 [555] Biology, NGS, Genomics
VCFtools 0.1.12a, 0.1.12b, 0.1.14 [556] Biology, SNPs
velvet 1.2.06, 1.2.07, 1.2.10 [557] Biology, Genomics, NGS
VEP 74 [558] Biology, NGS
VICUNA 1.3 [559] Biology, Assembly
Vim 7.4.5 [560] Programming, Scripting, Language
vmd 1.9.1 [561] Biology, Visualization
VSearch 20151022 [562] Biology, NGS
VTK 6.1.0 [563] Visualization, Graphics
Wannier90 1.2, 2.0.0 [564] Computational Physics
WebLogo 3.3 [565] Biology, Genomics
WDSSII 1 [566] Meteorology
WIEN2k 12.1 [567] Material Science, Chemistry
Wgs or Celera 8.2, 8.3rc1, 8.3rc1.r4638 [568] Biology, NGS
wublast 2.0 [569] Biology, Sequence Alignment
YAHA 0.1.82 [570] Biology NGS
XCrySDen 1.5.60 [571] Computational Material Science
Yambo 3.3.0 [572] Physics
YASM 1.3.0 [573] Computer Science
Yasra 2.32 [574] Biology, NGS
Zagros 1.0.0 [575] Biology, NGS
  1. ↑ Up to 3 most recent/important releases are listed. See the software wiki pages and the output of "module spider software" for full version listing.

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