Installed Software

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  • Last updated on 2017-02-09.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
Anvio 2.0.0, 2.0.2, 2.1.0 [18] Biology, Microbial 'omics
ANNOVAR 20120621, 20150322 [19] Biology, Genomics
AStalavista 3.2 [20] Biology, NGS, RNA-Seq, Genomics
ASTRID 20150807 [21] Biology, Genomics
Atlas 3.10.1, 3.11.17 [22] Library, Math
Amuse 6.0, 10.0 [23] Astrophysics
ANGSD 20150306, 20150909 [24] Biology, NGS
Affymetrix Power Tools 1.15.0, 1.18.0 [25] Biology, Genomics, Microarray
ARC 20140312 [26] Biology, NGS
Armadillo 6.200.3 [27] Library, C++ , Math
Astral 4.10.6, 4.10.7, 5.0.3 [28] Biology, Bioinformatics, NGS, Phylogenetics
AtomEye 3 [29] Material Science
ATRAM 20140624 [30] Biology, NGS
Augustus 2.6, 3.2.1, 3.2.2 [31] Biology, NGS
Auto3DEM 4.05.1, 4.05.2 [32] Image Reconstruction
BamBam 1.0 [33] Biology, NGS
BALI-PHY 2.3.8 [34] Bioinformatics, Bayesian Estimation
BAMM 2.5.0 [35] Biology, Phylogenetics
Bam-readcount 20150216 [36] Biology, NGS
Bamstats 20140602 [37] Biology, NGS
Bamtools 2.1.1 [38] Biology, NGS
BamUtil 1.0.2 [39] Biology, NGS
Bam-Readcount 20150616 [40]] Biology, Genomics
BAPS 6.0 [41] Biology, Populaton genetics
Barrnap 0.7 [42] Biology, RNA-Seq
Basemount 0.1.2.464 [43] Biology, DNA Sequencing
BayArea 1.0.2 [44] Biology
BayeScan 2.1 [45] Biology, SNP
BayeScEnv 1.1 [46]] Biology, SNP, Phylogenetics
BayesRate 1.3.43 [47] Biology, Phylogenetics
Bbcp 12.08.17.00.0 [48] Network file transfer
BBMap 36.23 [49] Biology, Alignment
Bcbio-nextgen 0.8.7, 0.9.9 [50] Biology, NGS
Bcftools 1.0, 1.2, 1.3.1 [51] Biology, Genomics, NGS
Bcl2fastq 2.16 [52] Biology, NGS, Illumina
BEAGLE 3.2.2, 4.0 [53] Biology, Genetics, Genotyping
BEAST 1.7.5, 1.8.1, 2.3.2 [54] Biology, Phylogenetics
Bedops 2.4.2 [55] Biology, Bioinformatics, Sequence, NGS
BEDTools 2.23.0, 2.24.0, 2.26.0 [56] Biology, NGS
BEST 2.3.1 [57] Biology, Phylogenetics
BESST 2.2.4 [58] Biology, Bioinformatics
BETA 1.0.5 [59] Biology, NGS
BFAST 0.7.0 [60] Biology, NGS
Bismark 0.7.4, 0.7.7, 0.13.0 [61] Biology, NGS, Methylation
BinPacker 1.0 [62] Biology, RNA-Seq, Sequence Assembly
BinSanity 0.1.3 [63] Biology, Genomics
Bioconductor Latest [64] Biology, R, Statistics
BioPerl 1.006901 [65] Biology, Perl
BioPython 1.59 [66] Biology, Python
BLASR 20130815 [67] Biology, NGS
NCBI BLAST 2.2.27, 2.5.0, 2.6.0 [68] Biology, Sequence alignment
Blast2go 2.5.0-20120705 [69] Biology, Annotation
BLAT 20120524 [70] Biology, Sequence alignment
Blender 2.63 [71] Graphics
BLESS 1.02 [72] Biology, NGS
BLUPF90 20160604 [73] Biology, Phylogenetics
BoltzTraP 1.2.5 [74] Physics
Boost 1.49.0, 1.53.0, 1.54.0 [75] C++, Library
Bowtie 0.12.9, 1.1.1, 1.2.0 [76] Biology, NGS
Bowtie2 2.2.8, 2.2.9, 2.3.0 [77] Biology, NGS
BPP 1.9.0, 2.2, 3.2 [78] Biology, Phylogenetics
BRANCH 1.8.1 [79] Biology, NGS, Mapping
BRATNextGen 20150505 [80] Biology, Genomics
BRIG 0.95 [81] Biology, Genomics
Bsoft 1.9.1 [82] Biology, Image Analysis
Bsmap 2.74, 2.87 [83] Biology, NGS, Methylation
BUCKy 1.4.4 [84] Biology, Genomics
BUSCO 1.1b1, 1.22, 2.0b [85] Biology, Genomics
Bwa 0.6.1, 0.7.12, 0.7.15 [86] Biology, NGS
BXH_XCEDE_tools 1.11.1 [87] Biology, Bioinformatics
Camino 20140723 [88] Biology, Neuroscience, Imaging
Canu 1.0, 1.1, 1.3 [89] Biology, Sequencing
CAP3 20120705 [90] Biology, Sequence Assembly
CASAVA 1.8.2 [91] Biology, NGS
CD-HIT 4.6, 4.6.4 [92] Biology, Genomics
CDO 1.6.1, 1.7.2rc5 [93] Climate
CEAS 1.0.2 [94] Biology, Genomics
CellProfiler 2.0 [95] Biology, Image Analysis
CellRanger 1.2.1 [96] Biology, Bioinformatics, NGS, RNA-Seq
CFITSIO 3.370 [97] Library, C
CGATools 1.6.0.42 [98] Biology, NGS
Charmm 36a3 [99] Simulation, Chemistry
Chartdirector 5.1.0 [100] Graphics
CheckM 1.0.4 [101] Biology, Genomics
Chimera 1.7 [102] Biology, Modeling
ChromEvol 2.0 [103] Biology, Phylogenetics
CIMS 4.1.2 [104] Biology, Genomics
Circos 0.63-pre11, 0.69-2 [105] Biology, Visualization
CisGenome 2.0 [106] Biology, Genomics, Peak Calling
Clann 3.2.3 [107] Biology, Phylogenetics
CLARK 1.2.2-b [108] Biology, Genomics
CLHEP 2.2.0.1 [109] High Energy Physics
CLIPper 1.0 [110] Biology, Sequencing
CLIPSeqTools 0.1.7 [111] Biology, Sequencing
ClonalFrame 1.1, 1.2 [112] Biology, Genomics, NGS
ClonalFrameML 1.25 [113] Biology, Genomics, NGS
ClustalW 2.1 [114] Biology, Genomics
Cluster3 1.52 [115] Biology, Genomics
Clview 20130402 [116] Biology, Genomics
ClustalO 1.2.0 [117] Biology, Genomics
ClusterFinder 313 [118] Biology, Metabolomics
CMake 2.8.8, 2.9.12.1, 3.1.0 [119] Programming, Build System
CMWP 140518 [120] Biology, Genomics
CNVnator 0.3.2 [121] Biology, Genomics
CNVSeq 20110715 [122] Biology, NGS
Cobrapy 0.3.2 [123] Biology, Metabolomics, Modeling
Coevol 1.3c, 1.4b [124] Biology, Phylogenetics
CoMap 1.4.1 [125] Biology, Genomics
CONSEL 0.20 [126] Biology, Phylogenetcs
CONCOCT 0.3.1 [127] Biology, Genomics
ContaVect 0.2 [128] Biology, Phylogenetics
CoNIFER 0.2.2 [129] Biology, Genomics
Consed 23.0 [130] Biology, Genomics
Coreutils 8.23 [131] GNU Utilities, Computer Science
covNMR 2014 [132] Biochemistry
CPLEX 12.6.5 [133] Optimizer
CUDA 4.2, 5.5 [134] Programming, Graphics
CrossMap 0.2.3 [135] Biology, Genomics
Crux 1.40 [136] Biology, Mass-Spectrometry
Cufflinks 1.3.0, 2.0.2, 2.2.1 [137] Biology, NGS
Cutadapt 1.7.1, 1.8.1, 1.10 [138] Biology, NGS
CUTE 20160116, 20161010 [139] Cosmology
Cytoscape 3.4.0 [140]] Biology, Bioinformatics
DAKOTA 5.4.0 [141] Computational Science
DaPars 0.9.0 [142] Biology, NGS, RNA-Seq
DALIGNER 1.0 [143] Biology, Sequencing
Datamash 1.1.0 [144] Math
DCMTK 3.6.0 [145] Biology, Neuroscience, Imaging
DSSAT 4.5 [146] Biology
dDocent 20160425 [147] Biology
DDSCAT 7.3.0 [148] Astrophysics
DDT 4.1.0, 4.2.1 [149] Software
Dealii 8.3.0 [150] Library
DeconSeq 0.4.3 [151] Biology, Phylogenetics
Delft3D 3621 [152] Hydrodynamics, Physics
DeepPicker 20161102 [153] Deep Learning, Cross-Molecule Training
Desmond 3.0.3.1 [154] Simulation, Biology, Chemistry
DETONATE 1.9, 1.11 [155] Biology, NGS
DEXTRACTOR 1.0 [156] Biology, Sequencing
Dalton 2011 [157] Quantum Chemistry
Diamond 0.5.1, 0.8.5 [158] Computational Biology, Genomics
Dibig Tools 1.0 [159] Bioinformatics, PBS, Torque, Jobs
DiffReps 1.55.4 [160] Biology, NGS, ChIP-Seq
Dindel 1.01 [161] Biology, NGS
DISCOVARdenovo 52488 [162] Biology, NGS
DIYABC 1.0.4.43b, 2.0.3 [163] Biology, Genomics
Dlpoly 4.03.4 [164] Simulation, Biology, Chemistry
Dlpoly-Classic 1.9 [165] Simulation, Biology, Chemistry
DNA Clust 3.0 [166] Biology, Genomics
Dock 6.5, 6.6, 6.7 [167] Chemistry, ligand binding prediction
DOT 2.0 [168] Biology, Bioinformatics, Docking
DosageConvertor 1.0.3 [169] Biology, Converter
Doxygen 1.8.3.1 [170] Programming, Documentation
DSSP 2.2.1 [171] Biology, Molecular Dynamics
DTI-TK 2.3.1 [172] Biology, Neurology, Imaging
EA-Utils 1.1.2.537 [173] Biology, NGS
ECTools 20140311, 20141201 [174] Biology, Sequencing, Bioinformatics
ECE 1.0 [175] Ece
EEGLAB 12.0.2.1b, 13.2.2b, 13.4.4b [176] Biology, Matlab
ED2 2.1 [177] Biology
eGene-MVN 0.1 [178] Biology, Genetics
eigenMT 20160228 [179] Biology, Genetics
EIGENSOFT 4.2, 5.0.1, 6.0.1 [180] Biology, Population
emboss 6.5.7 [181] Biology, multi-tool suite
EMAN2 2.11 [182] Biology
EMMAX 20100307 [183] Biology, NGS, Mapping
EMC 9.3.9 [184] Monte Carlo Simulations
EMIRGE 20130727 [185] Biology, NGS
Ensembl_Tools 80 [186] Biology, Bioinformatics
EPACTS 3.2.6 [187] Biology, Bioinformatics, Genomics
EPOCH 4.7.3 [188] Astronomy, CPPP
eQTLA 1.1 [189] Biology, Genomics
Eqtlbma 1.2.2 [190] Biology, Genotyping
Esmf 6.3.0rp1 [191] Climate
Espresso 5.0.1, 5.2.0, 5.2.1, 5.3.0 [192] Modeling, Physics
ESPRIT 201211 [193] Biology, NGS, Metagenomics
ETE2 2.1 [194] Biology, Phylogenetics
ETE3 3.0.0 [195] Biology, Phylogenetics
Eval 2.2.8 [196] Biology, Genomics, GUI
ExaBayes 1.4.1, 1.5 [197] Biology, Phylogenetics
ExaML 1.0.5, 1.0.12, 3.0.14, 3.0.17 [198] Biology, Phylogenetics
ExomeCNV 1.4 [199] Biology, NGS, Genomics
Exonerate 2.2.0 [200] Biology, Genomics
eXpress 1.3.1 [201] Biology, NGS
FALCON 20160828, 20161222 [202] Biology, Bioinformatics, NGS, Sequencing
FALCON_unzip 20160623, 20161222 [203] Biology, Bioinformatics
FAR 2.15 [204] Biology, Genomics
FASTA 34.26.5, 36.3.6d [205] Biology, Genomics
FAST-iCLIP 0.9.1 [206] Biology, Sequencing
FastML 3.0 [207] Biology, Phylogenetics, ML
FastQC 0.10.1, 0.11.2, 0.11.4 [208] Biology, NGS
Fastq-tools 0.7, 0.8 [209] Biology, NGS
FastStructure 20150112 [210] Biology, Genomics
FastTree 2.1.7 [211] Biology, Phylogenetics
Fastx_toolkit 0.0.13.2 [212] Biology, NGS
Fathmm 20150225 [213] Biology, Genomics
fcGENE 1.0.7 [214] Biology, Genomics, SNP
Ferret 6.82 [215] Oceanography, Meteorology
FFmpeg 2.1.3, 2.8.3 [216] Multimedia, audio, video
FFTW 3.3.2, 3.3.3, 3.3.4 [217] Math, Library, C++
FineSTRUCTURE 2.0.7 [218] Biology, Populatiopn Genetics
FLASH 1.2.10, 1.2.11 [219] Biology, Genomics, NGS
Flexbar 2.3 [220] Biology, Genomics, NGS
Fluent 14.5.7, 15.0.7, 16.0, 17.2 [221] Simulation, Fluid Dynamics
fqtools 20160224 [222] Biology, Bioinformatics, NGS
FragGeneScan 1.16 [223] Biology, NGS, Genomics
FrameDP 1.2.2 [224] Biology, Sequencing
Frealign 9.11 [225] Image Reconsctruction
FreeBayes 0.9.21, 1.0.1, 1.0.2 [226] Biology, NGS, SNP Calling
FREEC 9.6 [227] Biology, Sequencing
Freesurfer 5.2.0, 5.3.0 [228] Biology, Neurology, Imaging
FSL 5.0.2.2 [229] Biology, Neurology, Imaging
Galaxy latest [230] Biology, Chemistry, Other
GapFiller 1.11 [231] Biology, NGS
Garli 2.0, 2.01 [232] Biology, Phylogenetics
GAML 20150610 [233] Biology, NGS
GAMBIT 15.1.0, 16.0.0 [234] Game Theory
GARM 0.7.4 [235] Biology, NGS
GASVPro 201310 [236] Biology, NGS, Genomics
GATE 7.0 [237] Data Analysis
GATK 1.6.9, 3.4.46, 3.5.0 [238] Biology, NGS
Gaussian G03, G09-A.02, G09-C.01 [239] Modeling, Computational Chemistry
Gblocks 0.91b [240] Genomics, Alignment tool
GCTA 1.24.7, 1.26.0 [241] Biology, Genomics, SNP
GDAL 1.11.2 [242] Geospatial Data Modeling, Geospatial Library
GDC-Client 1.0.1 [243] Biology, Bioinformatics, Sequencing, NGS
Geant4 4.10 [244] Physics
GEM 20130406 [245] Biology, NGS
GEMINI 4.6.6a, 0.13.1, 0.18.0 [246] Biology, Genomics, Genetics
GenBank Tools 20140130 [247] Biology, Genomics
GeneMark 2012.04 [248] Biology, Genomics, Metagenomics
GeneSeqer 20140226 [249] Biology, Genomics
Genewise 2.2.0 [250] Biology, Genomics, Annotation
Genome STRiP 2.00.1602 [251] Biology, genomics, NGS
GenomicConsensus 20160523 [252] Biology, Phylogenetics
GenomicTools 2.7.0 [253] Biology, NGS
GenomeTools 1.5.7 [254] Biology, Bioinformatics
GenSel 4.90 [255] Biology, Genetics
GET_HOMOLOGUES 20150529 [256] Biology, Genomics
GFOLD 1.1.4 [257] Biology, RNA-seq
Gffread 0.9.8c [258] Biology, Bioinformatics
GKNO 1.30.18 [259] Biology, NGS,
Git 1.8.2.1, 1.9.0 [260] Development, Revision Control
Glimmer 3.02 [261] Biology, Microbial Annotation
Globus 2.1.3 [262] Data Transfer
GLPK 4.55 [263] Biology, Genomics
Gmap 20150723, 20160501, 20160816 [264] Biology, Genomics
GNU Compilers 5.2.0 [265] Compilers, Programming
GnuPlot 4.6.0, 5.0.3 [266] Graphics, Plotting, Programming
Grace 5.1.22 [267] Graphics, plotting, 2D
GrADS 2.0.1 [268] Earth Science
GramCluster 1.3 [269] Biology, Sequencing
GRASS 7.0 [270] Geography
GraphViz 2.38.0 [271] Graphics, plotting, visualization
GraphMap 0.4.0 [272] Biology, Sequencing
Gromacs 4.5.5, 4.6.5, 5.1.2 [273] Chemistry, Modeling, Simulation
GSNP 1.0 [274] Biology, Bioinformatics, NGS
GSL 1.15 [275] Library, Math, C++, C
Gsutil 4.15 [276] Cloud, Storage, Google
Gubbins 20150519, 20160421 [277] Biology, Phylogenetics, Genomics
GULP 4.0 [278] Material Science
HaMStR 13.2.2, 13.2.3, 13.2.4 [279] Biology, Genomics
HapCompass 0.7.7 [280] Biology, NGS, Genomics
HAPCUT 0.7 [281] Biology, Assembly
Hapsembler 2.21 [282] Biology, Genomics, NGS
HapTree 1.0 [283] Biology, Genomics, NGS
hapQTL 1.00 [284] Biology, Genomics
HDF4 4.2.11 [285] Library, Data
HDF5 1.8.9, 1.8.12, 1.8.15 [286] Library, Data
HGTFinder 20160720 [287] Biology, Genomics
HISAT2 2.0.0b, 2.0.1b, 2.0.3b [288] Biology, Sequence Alignment, NGS
HMMER3 3.0, 3.1b1, 3.1b2 [289] Biology, Genomics
HMMSplicer 0.9.5 [290] Biology, Genomics
HOMER 4.2, 4.7, 4.8 [291] Biology, Genomics
HOOMD 1.3.3 [292] Chemistry
HTMLDoc 1.2.82 [293] Documentation, PDF, HTML
HTSeq 0.5.3p3, 0.6.1p1 [294] Biology, NGS
Hyb 20141126 [295] Biology, NGS, RNA-Seq
HyPhy 2.1.2.28, 2.2.6.1 [296] Biology, Phylogenetics
Hypre 1.10.0b, 2.8.0b [297] Library, Math, Physics
iAssembler 1.32 [298] Biology, Assembly
IBDNe 20150815 [299] Biology, NGS
iCommands 3.3.1 [300] Biology, iPlant, Data Tansfer
ICORN2 0.95 [301] Biology, Sequencing
IDBA-UD 1.0.9, 1.1.0, 1.1.1 [302] Biology, NGS
IDBA-MT 1.0 [303] Biology, NGS
IEP 3.6 [304] Programming, Python, Editor
IGB 8.4.1 [305] Biology, Genomics, NGS
iGTP 1.1 [306] Biology, Bioinformatics, Phylogenetics
illumiprocessor 20150803 [307] Biology, Sequencing
IM and IMa 20091217 [308] Biology, Population
IMa2 20120827 [309] Biology, Population
ImageJ 1.48 [310] Image manipulation
ImageMagick 6.8.8-9 [311] Image manipulation
IMOD 4.7.15 [312] 3D modeling, Image Reconstruction
Intel Compilers 2016.0.109 [313] Programming, Compilers
IOAPI 3.1 [314] Meteorology
Iprscan 4.8 [315] Biology, Genomics
ipyrad 0.4.4 [316] Biology, bioinformatics, NGS
IQ-TREE 1.4.0, 1.4.2, 1.5.3 [317] Biology, Phylogenetics
IRAP 0.8.1p7 [318] Biology, NGS, RNA-seq
iRep 20161015 [319] Biology,
ITK 4.3.1 [320] Biology, Genomics
ITK-SNAP 3.0.0 [321] Biology, Neuroscience, Imaging
JAGS 3.3.0 [322] Statistics
Java 1.7.0_79, 1.8.0_31 [323] Java Development Kit
Je 1.0. [324] Biology, NGS
Jellyfish 2.1.1 [325] Biology, NGS
JModelTest 2.1.1 [326] Biology, Phylogenetics, Genomics
Julia 0.3.11, 0.4.6 [327] Programming, Languages
KaKs 1.2 [328] Biology, Phylogenetics
Kent 20120524 [329] Biology, NGS
Khmer 1.1, 2.0 [330] Biology, NGS
KIM 1.7.2 [331] Library
KING 1.4, 1.9 [332] Biology, Genomics
KisSplice 2.4.0-p1 [333] Biology, NGS
Kallisto 0.42.3, 0.42.4 [334] Biology, NGS, RNA-Seq
KERAS 1.0.8 [335] Deep Learning
Kmer 1934 [336] Biology, NGS
KmerGenie 1.6741 [337] Biology, NGS, Utilities
Kraken 0.10.4b [338] Biology, Genomics, Phylogenetics
Krona 20161019 [339] Biology, Bioinformatics
LAMMPS 15May15, 7Dec15, 30Jul16 [340] Molecular Dynamics Simulation
LAMP 2.5 [341] Biology, Genomics
Last 247, 531, 801 [342] Biology, Sequence alignment
Lastz 1.03.02, 1.02.00 [343] Biology, NGS
LDhat 2.2a [344] Biology, Genomics
LIBSVM 3.12 [345] Machine Learning
LIGR 2.05 [346] Biology, Assembly
LFMM 1.4 [347] Biology, Genomics
LSC 0.3, 0.3.1 [348] Biology, NGS, Error correction
Loci 3.3 [349] Fluid Dynamics
LoRMA 0.3 [350] Biology, NGS
LS-DYNA 700, 711, 800 [351] Physics
Lumpy 0.2.1 [352] Biology, SNP
LZO 2.09 [353] Library, Data Compression
MACH 1.0.18 [354] Biology, Genomics
Mach2VCF 20150515 [355] Biology
M5tools 20121126 [356] Biology, Bioinformatics, Genomics
MACS 1.4.2, 2.1.1 [357] Biology, ChIP-Seq
mafft 7.215, 7.245, 7.294 [358] Biology, Multiple sequence alignment
Mash 1.1 [359] Biology, Genomics
Maker 2.25b, 2.31.6, 2.31.8 [360] Biology, Annotation, Genomics
MapSplice 2.1.7 [361] Biology, NGS, RNA-Seq
MAPminer 1.1 [362] Biology, Phylogenetics
MassMine 0.9.5, 0.10.0, 0.11.0 [363] Data Mining
Maq 0.7.1 [364] Biology, NGS
MARK 2.0.1 [365] Statistics
MarkerMiner 20150429, 20150511 [366] Biology, Genomics
MaSuRCA 2.3.2, 3.2.1 [367] Biology, NGS
Matlab 2012a, 2013a, 2014a [368] Math, Simulation, Programming
MATS 2.1.0, 3.0.8, 3.0.9 [369] BIology, NGS
Mauve 2.3.1 [370] Biology, NGS
MaxBin 2.1.1 [371] Biology, NGS
MCarts 1.0.2 [372] Biology, Genomics, Markov models
MCNP 5, 6b2, 6 [373] Physics
MCNPX 2.7.0, 2.7.0-i8 [374] Physics
MEGAN 5.10.3, 6.4.15 [375] Biology, NGS
Megraft 1.0.2 [376] Biology, Sequencing
Melting 4.3.1 [377] Biology, Genome, RNA, Folding
Meme 4.11.1, 4.11.2 [378] Biology, Motifs, Sequence analysis
Meraculous 2.0.5 [379] Biology, NGS
Mercurial 4.0.2 [380] Development, Revision Control
Merlin 1.1.2 [381] Biogolgy, SNP
Meta-Tissue 0.4 [382] Biology, Genetics
Metabin 1.0 [383] Biology, Metagenomics
MetaCluster 5.0b [384] Biology, Metagenomics
MetaCV 2.3.0 [385] Biology, NGS
METAL 20110325 [386] Biology, Genomics
MetAMOS 1.5.0rc4-20140827 [387] Biology, Bioinformatics, Genomics, Assembly
Metassembler 1.5 [388] Biology, Genomics
MetaVelvet 1.2.01 [389] Biology, NGS
Metaxa2 2.0.2, 2.1.1 [390] Biology, NGS
MetaGeneMark 2012.04 [391] Biology, Genomics
Mfold 3.6 [392] Biology, Genomics
MGEScan 1.1 [393] Biology, Genomics
MHAP 1.6 [394] Biology, Sequencing
MIA 20130301 [395] Biology, NGS
MicrobeCensus 1.0.7 [396] Biology, NGS
MIDAS 20160830 [397] Biology, Phylogenetics
Midnight Commander 4.6.1 [398] Tools, Utilities
Migrate-n 3.3.0, 3.6.6, 3.6.11 [399] Biology, Population
Minced 0.2.0 [400] Biology, Genomics
Minimac 2-20140915, 3-20151015 [401] Biology, Genomics
mira 3.9.18, 4.0.rc1, 4.0.2 [402] Biology, NGS
MISO 0.4.9, 0.5.2, 0.5.3 [403] Biology, NGS
MMSEQ 1.0.8 [404] Biology, NGS
MSMBuilder 2.5.1 [405] Molecular Dynamics
MOABS 1.2.9, 1.3.2, 1.3.4 [406] Biology, NGS, Genomics
Modeller 9.11, 9.13, 9.14 [407] Biology, Modeling
Molden 5.0 [408] Molecular, electronic structure
MolPro 2012.1p22 [409] Quantum Chemistry, Ab Initio
mosaik 2.1.33, 2.2.3 [410] Biology,NGS
Mothur 1.36.1, 1.37.0, 1.38.1 [411] Biology, Microbial Ecology
MOTU 1.1 [412] Biology, Bioinformatics, Genomics
MPE2 2.4.9b [413] MPI
MP-EST 1.4, 1.5 [414] Biology, Phylogenetics
mpiP 3.4.1 [415] Parallel Computing
MrBayes 3.2.1, 3.2.4, 3.2.5 [416] Biology, Phylogenetics
MRIcron 201306 [417] Biology, MRI, Imaging
MUMmer 3.23 [418] Biology, Genomics
MUSCLE 3.8.31 [419] Biology, Genomics
MuTect 1.1.4, 1.1.7 [420] Biology, Genomics
MutSig 1.4, 1.41 [421] Biology, Genomics
MZMine 2.19, 2.20, 2.21 [422] Biology, Spectroscopy
NAMD 2.9, 2.11 [423] Simulation, Chemistry, Biology
Nanocorrect 20150727 [424] Biology, NGS
Nanopolish 20150904 [425] Biology
Nbody 6 [426] Astronomy
NCBI C++ Toolkit 12.0.0 [427] Biology, C++, Development
NCL 6.1.2, 6.3.0 [428] Atmosphere Science
NCO 4.2.1, 4.4.3 [429] Data exchange tools
Ncview 2.1.2 [430] Data visualization
NetCDF 3.4.2, 4.2, 4.3 [431] Data exchange, Tools
NEURON 7.4 [432] Biology, Neuroscience
Newbler 2.7, 2.8, 2.9 [433] Biology, NGS
Newick utils 1.6 [434] Biology, Phylogenetics
Nextallele 20140718 [435] Biology, Genomics
Nexus NCL 2.1.18 [436] Biology, Phylogenetics, Library
ngsCAT 0.1 [437] Biology, Bioinformatics, NGS
ngsTools 20150816 [438] Biology, NGS
NGSUtils 20130722, 20150206 [439] Biology, NGS
Nipype 0.10.0 [440] Biology, Bioinformatics, Neuroscience, Imaging
NMRPipe 7.9 [441] Biology, Biochemistry
Novoalign 2.08.02, 3.00.02 [442] Biology, NGS
NWChem 6.5, 6.6 [443] Chemistry
NxTrim 0.4.1 [444] Biology, Bioinformatics, NGS
Oases 0.2.08 [445] Biology, NGS
Olego 1.1.2, 1.1.5, 1.1.6 [446] Biology, NGS, RNA-Seq
OCaml 4.02.3 [447] Programming Languages, Scripting, Development
Octave 3.6.4 [448] Numerical Computation
Oncotator 1.5.2.0, 1.5.3.0, 1.8.0.0 [449] Biology, Genomics
OpenBabel 2.3.2 [450] Biology, Chemistry
OpenCL 1.1 [451] Programming, Library
OpenCV 2.4.8 [452] Computervision
OpenFOAM 2.1.1, 3.0.1, 4.0 [453] Fluid Dynamics
OpenMM 6.2.0 [454] Quantum Chemistry
Orange3 3.3.6 [455] Data Mining, Visualization
OrthoFinder 0.2.5, 0.6.0, 1.0.2 [456] Biology, Genomics
OrthoMCL 2.0.2, 2.0.3, 2.0.7 [457] Biology, Genomics
OTB 5.6.1 [458] Geospacial Imaging
p4vasp 0.3.29 [459] Molecular, Electronic Structure
Pacbio 2.2.0, 2.3.0p5 [460] Biology, Bioinformatics, NGS
Package-GFE 20150701 [461] Biology, Genomics
PALES 122 [462] Physics
PALADIN 1.3.1 [463] Biology, Phylogenetics
PAML 4.7, 4.8a, 4.9a [464] Biology, Phylogenetics
Pandaseq 20140808, 20150627 [465] Biology, Bioinformatics, NGS, Sequencing
PAPI 5.1.0.2 [466] Software, Computing
Parallel 20150122 [467] Programming, Languages
ParaView 4.1.0, 4.2.0, 4.3.0 [468] Data Analysis
Parsimonator 1.0.2 [469] Biology, Bioinformatics
PartitionFinder 1.1.1, 20161114-2.0.0 [470] Biology, Phylogenetics, Evolution
Parflow v615 [471] Ecology, Modeling
PASA 1.5, 2.0-r20150209 [472] Biology, Genomics
PASTA 20160616 [473] Biology, Sequence alignment,
PAUP 4.0b10, 4.1a147 [474] Biology, Phylogenetics
PAUDA 1.0.1 [475] Biology, Bioinformatics, Sequence alignment
PBalign 20160921 [476] Biology, Bioinformatics
PBCore 20151201 [477] Biology, Bioinformatics
PBCommand 20151203 [478] Biology, Library
PBJelly 14.7.14, 15.2.20, 15.8.24 [479] Biology, Bioinformatics
pbsdrmaa 1.0.17 [480] Libraries, Torque
p4est 1.1 [481] Library
pbsmrtpipe 20151202 [482] Biology
PeakSplitter 1.0 [483] Biology, Chip-Seq
PEAR 0.9.2, 0.9.6 [484] Biology, NGS
PDT 3.18, 3.20, 3.22 [485] Programming, Profiler
Perl 5.16.0 [486] Programming, Language
PerM 0.4.0 [487] Biology, NGS
PETSc 2.3, 3.3 [488] Math, Numerical solvers
PGDSpider 2.0.9.0 [489] Biology, NGS
Phenix 1.8.1069, 1.10.2155 [490] Crystallography
PHYLDOG 20130418 [491] Biology, Genomics, Phylogenetics
Phyluce 20140427, 20151103, 20160715 [492] Biology, Phylogenetics
Phyutility 2.7.1 [493] Biology, Bioinformatics
PfamScan 1.3 [494] Biology, Genomics
PHITS 2.52, 2.76. 2.82 [495] Physics
PIPE-CLIP 1.1.0 [496] Biology, NGS
Pipits 1.3.6 [497] Biology, Sequencing
piPipes 1.5.0 [498] Biology, Phylogenetics
Phonopy 1.9.2 [499] Chemistry
PHYLIP 3.696 [500] Biology, Phylogenetics
PhyloBayes 3.3f, 1.4f MPI [501] Biology, Phylogenetics
PhyloNet 3.5.7 [502] Biology, Phylogenetics
Phylosift 1.1 [503] Biology, Genomics, Phylogenetics, Taxonomy
PhyML 3.0, 3.1 [504] Biology, Phylogenetics
Picard 1.72, 1.80, 2.0.1 [505] Biology, NGS
PICRUSt 1.0.0, 1.1.0 [506] Biology, Phylogenetics
Piranha 1.2.1 [507] Biology, Phylogenetics
PLAST 1.0 [508] Biology, Bioinformatics
Platypus 0.8.1 [509] Biology, NGS
Plink 1.07, 1.90b3, 1.90b3.39 [510] Biology, GWAS
PLINKSEQ 0.10 [511] Biology, Genomics
PluMiST 1.1 [512] Biology, Phylogenetics, Genomics
PolyPhen 2.2.2.r405b [513] Biology, Genomics
PonyTools 0.1 [514] Biology, Genomics
Poretools 0.5.0 [515] Biology, Sequencing
POV-Ray 3.7 [516] 3D, Graphics
Prank 20150803 [517] Biology, Bioinformatics, Alignment
Preseq 0.0.4 [518] Biology, NGS
PRICE 1.2 [519] Biology, NGS
Primer3 2.3.4 [520] Biology, Genomics
PRIMUS 1.8.0 [521] Biology, Phylogenetics
PRINSEQ 0.20.4 [522] Biology, Sequencing
Prodigal 2.6.3 [523] Biology, Genomics
ProfessAtQE 2014 [524] Material Science, Molecular Dynamics
Prokka 1.10, 1.11 [525] Biology, Genomics, Bioinformatics, Assembly
ProBABEL 0.4.2, 0.4.3, 0.4.5 [526] Biology, Genomics, GWAS
Probalign 1.4 [527] Biology, Genomics
Proovread 1.03rcl [528] Biology, Genomics, NGS
Proteinortho 4.26, 5.11 [529] Biology, Genomics
PROVEAN 1.1.5 [530] Biology, Genomics
PyAni 0.2.1 [531] Bilogy, Genomics
PyHDF 0.9.0 [532] Library, HDF4
Python 2.7.6, 3.5.0 [533] Biology, Genomics, NGS
Pyfasta 0.5.2 [534] Biology, Phylogenetics
Pyrad 3.0.63 [535] Biology, Sequencing Alignment, Assembly
QDD 3.1.2 [536] Programming, scripting, language
QGIS 2.18.0 [537] Geography
QIIME 1.9.0, 1.9.1 [538] Biology, Ecology
QIIME2 2.0.6 [539] Biology, Ecology
QT 4.8.3 [540] Computer Science
QUAST 2.3, 4.4 [541] Biology, NGS
Quake 0.3 [542] Biology, Sequencing
Quantas 1.0.4, 1.0.8 [543] Biology, Bioinformatics, NGS
QualiMap 2.1.1 [544] Biology, Sequence alignment
Quickquartet 1.0.0 [545] Biology, Phylogenetics
R Rmpi/3.3.1, 3.2.0, 3.3.0 [546] Statistics, Programming
R2R 1.0.4 [547] Biology, RNA
R8S 1.71, 1.8 [548] Biology, Evolution
Racon 20161013 [549] Biology, Sequencing
RADICAL 0.2 [550] Biology, Phylogenetics, Genomics
Randfold 2.0.1 [551] Biology, RNA
Rascaf 1.0.2 [552] Biology, RNA-Seq
RAxML 8.1.23, 8.2.2, 8.2.3 [553] Biology, Phylogenetics
Ray 2.3.1 [554] Biology, Genomics, NGS
REAGO 1.1 [555] Biology, Assembly
REAPR 1.0.18 [556] Biology, Bioinformatics, Assembly
RELION 1.4 [557] Biology, Bioinformatics
RepeatExplorer 20150506 [558] Biology, Genomics
RepeatMasker 3.3.0 [559] Biology, Genomics
RepeatModeler 1.0.8 [560] Biology, Bioinformatics
Reptile 1.1 [561] Biology, NGS, error correction
RevBayes 1.0.0, 1.0.3 [562] Biology, Phylogenetics
riboPicker 0.4.3 [563] Biology, Sequence
RNAhybrid 2.1.1 [564] Biology, Genomics
rRNASelector 1.0.0 [565] Biology, Sequencing
rnaQUAST 1.2.0 [566] Biology, NGS, Sequencing
ROOT 6.0 [567] Data Analysis
Roary 3.4.1 [568] Biology, Genomics
Rosetta 2014wk4 [569] Biology, Structure, Modelling
RSEG 0.4.8 [570] Biology, NGS
RSEM 1.2.19, 1.2.28, 1.2.29 [571] Biology, NGS, RNA-Seq
RSeQC 2.3.7, 2.6.2 [572] Biology, NGS, RNA-Seq
RStudio 0.99.902, 0.99.903 [573] R, Statistics, Programming
RTGTools 3.7.1 [574] Biology, NGS
Ruby 1.9.3-p0 [575] Programming, Scripting, Language
Sailfish 0.6.3 [576] Biology, NGS, RNA-Seq
Salmon 0.6.0, 0.7.2 [577] Biology, RNA-seq
Sambamba 0.5.0-dev, 0.5.10, 0.6.3 [578] Biology, NGS
Samstat 1.08 [579] Biology, NGS, Bioinformatics, Sequencing
Samblaster 0.1.14 [580] Biology, NGS
samtools 1.1, 1.2, 1.3.1 [581] Biology, NGS
SAS 9.3 [582] Statistics, Graphing
SATe 2.2.7 [583] Biology, Phylogenetics
Scala 2.11.5 [584] Programming, Language
Scalablast 2.4.53 [585] Biology, Genomics
Scalpel 0.1.1 [586] Biology, NGS
SCRIPTURE 20101211 [587] Biology, Bioinformatics, Genomics
Shannon 20160211 [588] Biology, RNA-Seq
SHAPEIT 2.5.5 [589] Biology, SNP
SHAPE-MaP 1.2 [590] Biology, Phylogenetics
Sharcgs 1.2.11 [591] Biology, NGS, Assembly
SHEsisPlus 1.0 [592] Biology, Phylogenetics
shustring 2.6 [593] Biology, Sequencing
SCons 2.3.0 [594] Programming
Scoary 1.6.10 [595] Biology, Bioinformatics, Genomics
SCRATCH1D 1.0 [596] Biology, Genomics
Scythe 0.991 [597] Biology, NGS
SDT 1.2 [598] Biology, Sequencing
Segemehl 0.1.9 [599] Biology, NGS, Mapper
SEPP 1.0, 3.0 [600] Biology, Phylogenetics, HMM
SGA 0.10.14 [601] Biology, Assembly
Seq-Gen 1.3.3 [602] Biology, Phylogenetics
SeqPrep 0.5 [603] Biology, NGS
Seqmagick 20150923 [604] Biology, Phylogenetics
SeqMap 1.0.13 [605] Biology, NGS
Seqtk 20140729 [606] Biology, NGS
SEQuel 1.0.1 [607] Biology, NGS
SeqyClean 1.8.10 [608] Biology, NGS, Bioinformatics
ShoRAH 20131204 [609] Biology, NGS, quality filter
SHRiMP 2.2.3 [610] Biology, NGS
SICER 1.1 [611] Biology, ChIP-Seq
Sickle 1.200, 1.33 [612] Biology, NGS, quality filter
Siesta 2.0.2,3.1 [613] Simulation, Physics, Ab Initio
SIFT 4.0.3b [614] Biology, Genomics
SignalP 4.1c [615] Biology, NGS
Silo 4.7 [616] Library, Data
SIPeS 2.0 [617] Biology, Bioinformatics, ChIP-Seq
Slicer 4.3.1 [618] Biology, Imaging
SMALT 0.7.6 [619] Biology, NGS
Snap 20100728 [620] Biology, Genomics
SNAPE-pooled 20130407 [621] Biology, SNP
SNeP 1.1 [622] Biology, Phylogenics
SnpEff 4.1i, 4.2, 4.3 [623] Biology, NGS, Genomics
SNPhylo 20140701 [624] Bilogy, Phylogenetics
SNP-sites 2.0.3 [625] Biology, SNP
Snippy 20160419 [626] Biology, Phylogenetics
SOAPdenovo 1.05 [627] Biology, NGS
SOAPdenovo-Trans 1.01, 1.03 [628] Biology, NGS
SOAPec 2.03 [629] Biology, Phylogenetics
SOAPsplice 1.10 [630] Biology, NGS
SortMeRNA 2.1 [631] Biology, Sequencing, NGS
SparCC 201402 [632] Microbial Ecology
Spades 3.8.0, 3.9.0, 3.10.0 [633] Biology, NGS
Spanki 0.4.1, 0.4.3, 0.5.0 [634] Biology, NGS, RNA-Seq
SPARTA+ 2.60 [635] Chemistry
Spidey 20150922 [636] Biology, Genomics
SPIMAP 1.1 [637] Biology, Phylogenetics
SpliceTrap 0.90.5 [638] Biology, NGS, RNA-Seq
SPM 8 [639] Biology, Statistics, Neurology, Imaging
Sputnik 1.0 [640] Biology, Genomics
SQLite 3.8.8.2 [641] Database
SQL_Developer 4.1.2 [642] Programming, Oracle, Sql
SRA 2.1.10 [643] biology, NGS
SSPACE 2.0, 3.0 [644] Biology, NGS
SST-Core 6.0.0 [645] MPI
SSR_pipeline 0.951 [646] Bilogy, DNA Sequencing
Stacks 1.21, 1.24, 1.35 [647] Biology, Genomics, NGS
Staden 1.14.6 [648] Biology, Sequencing
STAR 2.4.0j, 2.5.1b [649] Biology, NGS, Alignment
STAR-CCM+ 8.06 [650] Mechanical Engineering
Stata 10.1, 13 [651] Statistics, Data analysis
Stringtie 1.0.0, 1.1.2, 1.2.1 [652] Biology, NGS, Alignment
Structure 2.3.3, 2.3.4 [653] Biology, Population
Subread 1.5.0-p1, 1.5.1 [654] Biology, Sequencing, SNP
SUNDIALS 2.3.0, 2.5.0 [655] Numerical Solver
SVDetect 0.8b [656] Biology, NGS, SNP
swak4Foam 2.x [657] Fluid Dynamics
swarm 1.2.11 [658] Data Analysis
SWEEP 20160722 [659] Biology, SNP
Swig 2.0.9 [660] Programming, C, C++, Python
SwitchSeq 20140907 [661] Biology, NGS
Syzygy 1.2.7 [662] Biology, Genomics
TetGen 1.5.0 [663] Tetrahedral Meshes 3D
tapir 20160825 [664] Biology, Phylogenetics
TAPIS 1.2.1 [665] Biology, Sequencing
TASSEL 5.0, 5.2.29 [666] Biology, Genomics
TAU 2.21.4, 2.23, 2.24, 2.52 [667] Profiling, Tracing, Programming
taxMap 0.1 [668] Biology, Phylogenetics, Taxonomy
T-Coffee 9.03.r1318 [669] Biology, Genomics, Multiple Alignment
TensorFlow 0.10.0 [670] Library, Math
TESS 2.3.1 [671] Biology, Genomics, Markov
tgicl 2.1 [672] Biology, sequencing, clustering
Tmux 2.0 [673] GNU, Terminal Multiplexer
TomoPy 0.0.3 [674] Biology, Neuroimaging
Tophat 1.4.1, 2.0.13, 2.1.0 [675] Biology, NGS
Torch 20160704 [676] Lua
Totalview 8.12.0 [677] Computer Science
TPP 4.7.0 [678] Bioinformatics, MassSpec
TrackTools 2011 [679] Bioinformatics
TrackVis 0.5.2.2 [680] Biology, Spectroscopy
Tracula 5.3.2014_05_26 [681] Biology, Bioinformatics, Neuroscience, Imaging
TraitRate 1.1 [682] Biology, Evolution
Trans-ABySS 1.5.4 [683] Biology, Phylogenetics
TransDecoder 20140704, 2.0.1, 3.0.0 [684] Biology, NGS
Transrate 1.0.1 [685] Biology, Assembly
TraCeR 20160519 [686] Biology, Bioinformatics
TreeCorr 3.2.3 [687] Physics
TreeFix 1.1.7, 1.1.10 [688] Biology, Phylogenetics
TreeMix 1.12 [689] Biology, Phylogenetics
TreePL 20150305 [690] Biology, Phylogenetics
TriMetAss 1.1 [691] Biology, Bioinformatics, NGS
TRF 4.04 [692] Biology, Genomics
Trilinos 11.4.1, 11.8.1 [693] Math Algorithm
trimAl 1.2 [694] Biology, Genomics, Sequence Alignment
Trim Galore 0.2.8, 0.4.1 [695] Biology, NGS
Trimmomatic 0.32, 0.33, 0.36 [696] Biology, NGS
Trinity r20160329-2.2.0, r20161120-2.3.2 [697] Biology, NGS, RNA-Seq
Trinotate 2.0.1, 3.0.1 [698] Biology
TRNAscan-SE 1.23 [699] Biology, NGS, Bioinformatics
Twinscan 4.1.2 [700] Biology, Genomics
usearch 7.0.1001-64, 8.0.1517, 9.2.64 [701] Biology, Sequence analysis
UDUNITS 2.2.17 [702] Library, Units, Programming
UFITS 0.7.2 [703] Biology, NGS
UNAFold 3.8 [704] Biology, Genome, RNA, Folding
UProC 1.2.0 [705] Biology, Genomics
Valgrind 3.9.0 [706] Computer Science
VarDictJava 20160521 [707] Biology, NGS
VarScan 2.3.6 [708] Biology, NGS, Genomics
VASP 5.3.2, 5.3.3, 5.3.5, 5.4.1 [709] Quantum Chemistry, Ab Initio
VAST-TOOLS 20150506 [710] Biology, NGS, RNA-Seq
VCFLib 20141119, 20150313 [711] Biology, NGS, Genomics
VCFtools 0.1.12a, 0.1.12b, 0.1.14 [712] Biology, SNPs
velvet 1.2.06, 1.2.07, 1.2.10 [713] Biology, Genomics, NGS
VEP 74, 83 [714] Biology, NGS
VICUNA 1.3 [715] Biology, Assembly
ViennaRNA 2.2.6 [716] Biology, RNA-seq
Vim 7.4.5 [717] Programming, Scripting, Language
vmd 1.9.1 [718] Biology, Visualization
VSearch 20151022, 20161209-2.3.4 [719] Biology, NGS
VT 20140903, 20160129 [720] Biology, Genomics
VTK 6.1.0 [721] Visualization, Graphics
V-Phaser2 02112013 [722] Biology, Phylogenetics
Virsorter 1.0.3 [723] Biology, Phylogenetics
w2rap-contiger 20161124 [724] Biology, Genomics
Wannier90 1.2, 2.0.0 [725] Computational Physics
WebLogo 3.3 [726] Biology, Genomics
WEVOTE 1.5.0 [727] Biology, Genomics
WDSSII 1 [728] Meteorology
WIEN2k 12.1 [729] Material Science, Chemistry
Wgs or Celera 8.2, 8.3rc1, 8.3rc1.r4638 [730] Biology, NGS
wublast 2.0 [731] Biology, Sequence Alignment
YAHA 0.1.82 [732] Biology NGS
XCrySDen 1.5.60 [733] Computational Material Science
Yambo 3.3.0 [734] Physics
YASM 1.3.0 [735] Computer Science
Yasra 2.32 [736] Biology, NGS
Zagros 1.0.0 [737] Biology, NGS
Zeo++ 0.2.2 [738] Chemistry
Zorro 2.2 [739] Biology, Sequencing
  1. 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.

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