Installed Software

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  • Last updated on 2016-10-31.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
ALE 20150507 [10] Biology, Bioinformatics, Assembly
ALLPATHS-LG 42316, 44837 [11] Biology, NGS
Amber 11, 12, 14, 16 [12] Simulation, chemistry
AMAS 0.98 [13] Biology, Sequence Alignment
AMOS 3.1.0 [14] Biology, Genomics, NGS
AMPHORA2 20140305 [15] Biology, Phylogenetics
Anvio 2.0.0, 2.0.2 [16] Biology, Microbial 'omics
ANNOVAR 20120621, 20150322 [17] Biology, Genomics
AStalavista 3.2 [18] Biology, NGS, RNA-Seq, Genomics
ASTRID 20150807 [19] Biology, Genomics
Atlas 3.10.1, 3.11.17 [20] Library, Math
Amuse 6.0, 10.0 [21] Astrophysics
ANGSD 20150306, 20150909 [22] Biology, NGS
Affymetrix Power Tools 1.15.0, 1.18.0 [23] Biology, Genomics, Microarray
ARC 20140312 [24] Biology, NGS
Armadillo 6.200.3 [25] Library, C++ , Math
Astral 4.8.0, 4.10.6, 4.10.7 [26] Biology, Bioinformatics, NGS, Phylogenetics
AtomEye 3 [27] Material Science
ATRAM 20140624 [28] Biology, NGS
Augustus 2.6, 3.2.1 [29] Biology, NGS
Auto3DEM 4.05.1, 4.05.2 [30] Image Reconstruction
BamBam 1.0 [31] Biology, NGS
BALI-PHY 2.3.8 [32] Bioinformatics, Bayesian Estimation
BAMM 2.5.0 [33] Biology, Phylogenetics
Bam-readcount 20150216 [34] Biology, NGS
Bamstats 20140602 [35] Biology, NGS
Bamtools 2.1.1 [36] Biology, NGS
BamUtil 1.0.2 [37] Biology, NGS
Bam-Readcount 20150616 [38]] Biology, Genomics
BAPS 6.0 [39] Biology, Populaton genetics
Barrnap 0.7 [40] Biology, RNA-Seq
Basemount 0.1.2.464 [41] Biology, DNA Sequencing
BayArea 1.0.2 [42] Biology
BayesRate 1.3.43 [43] Biology, Phylogenetics
Bbcp 12.08.17.00.0 [44] Network file transfer
BBMap 36.23 [45] Biology, Alignment
Bcbio-nextgen 0.8.7, 0.9.9 [46] Biology, NGS
Bcftools 1.0, 1.2, 1.3.1 [47] Biology, Genomics, NGS
Bcl2fastq 2.16 [48] Biology, NGS, Illumina
BEAGLE 3.2.2, 4.0 [49] Biology, Genetics, Genotyping
BEAST 1.7.5, 1.8.1, 2.3.2 [50] Biology, Phylogenetics
Bedops 2.4.2 [51] Biology, Bioinformatics, Sequence, NGS
BEDTools 2.23.0, 2.24.0, 2.26.0 [52] Biology, NGS
BEST 2.3.1 [53] Biology, Phylogenetics
BESST 2.2.4 [54] Biology, Bioinformatics
BETA 1.0.5 [55] Biology, NGS
BFAST 0.7.0 [56] Biology, NGS
Bismark 0.7.4, 0.7.7, 0.13.0 [57] Biology, NGS, Methylation
BinPacker 1.0 [58] Biology, RNA-Seq, Sequence Assembly
BinSanity 0.1.3 [59] Biology, Genomics
Bioconductor Latest [60] Biology, R, Statistics
BioPerl 1.006901 [61] Biology, Perl
BioPython 1.59 [62] Biology, Python
BLASR 20130815 [63] Biology, NGS
NCBI BLAST 2.2.27, 2.2.29, 2.5.0 [64] Biology, Sequence alignment
Blast2go 2.5.0-20120705 [65] Biology, Annotation
BLAT 20120524 [66] Biology, Sequence alignment
Blender 2.63 [67] Graphics
BLESS 1.02 [68] Biology, NGS
BLUPF90 20160604 [69] Biology, Phylogenetics
BoltzTraP 1.2.5 [70] Physics
Boost 1.49.0, 1.53.0, 1.54.0 [71] C++, Library
Bowtie 0.12.9, 1.0.0, 1.1.1 [72] Biology, NGS
Bowtie2 2.2.6, 2.2.8, 2.2.9 [73] Biology, NGS
BPP 1.9.0, 2.2, 3.2 [74] Biology, Phylogenetics
BRANCH 1.8.1 [75] Biology, NGS, Mapping
BRATNextGen 20150505 [76] Biology, Genomics
BRIG 0.95 [77] Biology, Genomics
Bsoft 1.9.1 [78] Biology, Image Analysis
Bsmap 2.74, 2.87 [79] Biology, NGS, Methylation
BUCKy 1.4.4 [80] Biology, Genomics
BUSCO 1.1b1, 1.22 [81] Biology, Genomics
Bwa 0.6.1, 0.7.12, 0.7.15 [82] Biology, NGS
BXH_XCEDE_tools 1.11.1 [83] Biology, Bioinformatics
Camino 20140723 [84] Biology, Neuroscience, Imaging
Canu 1.0, 1.1, 1.3 [85] Biology, Sequencing
CAP3 20120705 [86] Biology, Sequence Assembly
CASAVA 1.8.2 [87] Biology, NGS
CD-HIT 4.6, 4.6.4 [88] Biology, Genomics
CDO 1.6.1, 1.7.2rc5 [89] Climate
CEAS 1.0.2 [90] Biology, Genomics
CellProfiler 2.0 [91] Biology, Image Analysis
CFITSIO 3.370 [92] Library, C
CGATools 1.6.0.42 [93] Biology, NGS
Charmm 36a3 [94] Simulation, Chemistry
Chartdirector 5.1.0 [95] Graphics
CheckM 1.0.4 [96] Biology, Genomics
Chimera 1.7 [97] Biology, Modeling
ChromEvol 2.0 [98] Biology, Phylogenetics
CIMS 4.1.2 [99] Biology, Genomics
Circos 0.63-pre11, 0.69-2 [100] Biology, Visualization
CisGenome 2.0 [101] Biology, Genomics, Peak Calling
Clann 3.2.3 [102] Biology, Phylogenetics
CLARK 1.2.2-b [103] Biology, Genomics
CLHEP 2.2.0.1 [104] High Energy Physics
CLIPper 1.0 [105] Biology, Sequencing
CLIPSeqTools 0.1.7 [106] Biology, Sequencing
ClonalFrame 1.1, 1.2 [107] Biology, Genomics, NGS
ClonalFrameML 1.25 [108] Biology, Genomics, NGS
ClustalW 2.1 [109] Biology, Genomics
Cluster3 1.52 [110] Biology, Genomics
Clview 20130402 [111] Biology, Genomics
ClustalO 1.2.0 [112] Biology, Genomics
ClusterFinder 313 [113] Biology, Metabolomics
CMake 2.8.8, 2.9.12.1, 3.1.0 [114] Programming, Build System
CMWP 140518 [115] Biology, Genomics
CNVnator 0.3.2 [116] Biology, Genomics
CNVSeq 20110715 [117] Biology, NGS
Cobrapy 0.3.2 [118] Biology, Metabolomics, Modeling
Coevol 1.3c, 1.4b [119] Biology, Phylogenetics
CoMap 1.4.1 [120] Biology, Genomics
CONSEL 0.20 [121] Biology, Phylogenetcs
CONCOCT 0.3.1 [122] Biology, Genomics
CoNIFER 0.2.2 [123] Biology, Genomics
Consed 23.0 [124] Biology, Genomics
Coreutils 8.23 [125] GNU Utilities, Computer Science
covNMR 2014 [126] Biochemistry
CPLEX 12.6.5 [127] Optimizer
CUDA 4.2, 5.5 [128] Programming, Graphics
CrossMap 0.2.3 [129] Biology, Genomics
Crux 1.40 [130] Biology, Mass-Spectrometry
Cufflinks 1.3.0, 2.0.2, 2.2.1 [131] Biology, NGS
Cutadapt 1.7.1, 1.8.1, 1.10 [132] Biology, NGS
CUTE 20160116, 20161010 [133] Cosmology
DAKOTA 5.4.0 [134] Computational Science
DaPars 0.9.0 [135] Biology, NGS, RNA-Seq
DALIGNER 1.0 [136] Biology, Sequencing
Datamash 1.1.0 [137] Math
DCMTK 3.6.0 [138] Biology, Neuroscience, Imaging
DSSAT 4.5 [139] Biology
dDocent 20160425 [140] Biology
DDSCAT 7.3.0 [141] Astrophysics
DDT 4.1.0, 4.2.1 [142] Software
Dealii 8.3.0 [143] Library
DeconSeq 0.4.3 [144] Biology, Phylogenetics
Delft3D 3621 [145] Hydrodynamics, Physics
Desmond 3.0.3.1 [146] Simulation, Biology, Chemistry
DETONATE 1.9, 1.11 [147] Biology, NGS
DEXTRACTOR 1.0 [148] Biology, Sequencing
Dalton 2011 [149] Quantum Chemistry
Diamond 0.5.1, 0.8.5 [150] Computational Biology, Genomics
Dibig Tools 1.0 [151] Bioinformatics, PBS, Torque, Jobs
DiffReps 1.55.4 [152] Biology, NGS, ChIP-Seq
Dindel 1.01 [153] Biology, NGS
DISCOVARdenovo 52488 [154] Biology, NGS
DIYABC 1.0.4.43b, 2.0.3 [155] Biology, Genomics
Dlpoly 4.03.4 [156] Simulation, Biology, Chemistry
Dlpoly-Classic 1.9 [157] Simulation, Biology, Chemistry
DNA Clust 3.0 [158] Biology, Genomics
Dock 6.5, 6.6, 6.7 [159] Chemistry, ligand binding prediction
DOT 2.0 [160] Biology, Bioinformatics, Docking
DosageConvertor 1.0.3 [161] Biology, Converter
Doxygen 1.8.3.1 [162] Programming, Documentation
DSSP 2.2.1 [163] Biology, Molecular Dynamics
DTI-TK 2.3.1 [164] Biology, Neurology, Imaging
EA-Utils 1.1.2.537 [165] Biology, NGS
ECTools 20140311, 20141201 [166] Biology, Sequencing, Bioinformatics
EEGLAB 12.0.2.1b, 13.2.2b, 13.4.4b [167] Biology, Matlab
ED2 2.1 [168] Biology
eGene-MVN 0.1 [169] Biology, Genetics
eigenMT 20160228 [170] Biology, Genetics
EIGENSOFT 4.2, 5.0.1, 6.0.1 [171] Biology, Population
emboss 6.5.7 [172] Biology, multi-tool suite
EMAN2 2.11 [173] Biology
EMMAX 20100307 [174] Biology, NGS, Mapping
EMC 9.3.9 [175] Monte Carlo Simulations
EMIRGE 20130727 [176] Biology, NGS
Ensembl_Tools 80 [177] Biology, Bioinformatics
EPACTS 3.2.6 [178] Biology, Bioinformatics, Genomics
EPOCH 4.7.3 [179] Astronomy, CPPP
eQTLA 1.1 [180] Biology, Genomics
Eqtlbma 1.2.2 [181] Biology, Genotyping
Esmf 6.3.0rp1 [182] Climate
Espresso 5.0.1, 5.2.0, 5.2.1, 5.3.0 [183] Modeling, Physics
ESPRIT 201211 [184] Biology, NGS, Metagenomics
ETE2 2.1 [185] Biology, Phylogenetics
Eval 2.2.8 [186] Biology, Genomics, GUI
ExaBayes 1.4.1 [187] Biology, Phylogenetics
ExaML 1.0.5, 1.0.12, 3.0.14, 3.0.17 [188] Biology, Phylogenetics
ExomeCNV 1.4 [189] Biology, NGS, Genomics
Exonerate 2.2.0 [190] Biology, Genomics
eXpress 1.3.1 [191] Biology, NGS
FALCON 20160516, 20160828 [192] Biology, Bioinformatics, NGS, Sequencing
FALCON_unzip 20160623 [193] Biology, Bioinformatics
FAR 2.15 [194] Biology, Genomics
FASTA 34.26.5, 36.3.6d [195] Biology, Genomics
FAST-iCLIP 0.9.1 [196] Biology, Sequencing
FastML 3.0 [197] Biology, Phylogenetics, ML
FastQC 0.10.1, 0.11.2, 0.11.4 [198] Biology, NGS
Fastq-tools 0.7, 0.8 [199] Biology, NGS
FastStructure 20150112 [200] Biology, Genomics
FastTree 2.1.7 [201] Biology, Phylogenetics
Fastx_toolkit 0.0.13.2 [202] Biology, NGS
Fathmm 20150225 [203] Biology, Genomics
fcGENE 1.0.7 [204] Biology, Genomics, SNP
Ferret 6.82 [205] Oceanography, Meteorology
FFmpeg 2.1.3, 2.8.3 [206] Multimedia, audio, video
FFTW 3.3.2, 3.3.3, 3.3.4 [207] Math, Library, C++
FineSTRUCTURE 2.0.7 [208] Biology, Populatiopn Genetics
FLASH 1.2.10, 1.2.11 [209] Biology, Genomics, NGS
Flexbar 2.3 [210] Biology, Genomics, NGS
Fluent 14.5.7, 15.0.7, 16.0, 17.2 [211] Simulation, Fluid Dynamics
fqtools 20160224 [212] Biology, Bioinformatics, NGS
FragGeneScan 1.16 [213] Biology, NGS, Genomics
FrameDP 1.2.2 [214] Biology, Sequencing
Frealign 9.11 [215] Image Reconsctruction
FreeBayes 0.9.21, 1.0.1, 1.0.2 [216] Biology, NGS, SNP Calling
FREEC 9.6 [217] Biology, Sequencing
Freesurfer 5.2.0, 5.3.0 [218] Biology, Neurology, Imaging
FSL 5.0.2.2 [219] Biology, Neurology, Imaging
Galaxy latest [220] Biology, Chemistry, Other
GapFiller 1.11 [221] Biology, NGS
Garli 2.0, 2.01 [222] Biology, Phylogenetics
GAML 20150610 [223] Biology, NGS
GAMBIT 15.1.0, 16.0.0 [224] Game Theory
GARM 0.7.4 [225] Biology, NGS
GASVPro 201310 [226] Biology, NGS, Genomics
GATE 7.0 [227] Data Analysis
GATK 1.6.9, 3.4.46, 3.5.0 [228] Biology, NGS
Gaussian G03, G09-A.02, G09-C.01 [229] Modeling, Computational Chemistry
Gblocks 0.91b [230] Genomics, Alignment tool
GCTA 1.24.7 [231] Biology, Genomics, SNP
GDAL 1.11.2 [232] Geospatial Data Modeling, Geospatial Library
GDC-Client 1.0.1 [233] Biology, Bioinformatics, Sequencing, NGS
Geant4 4.10 [234] Physics
GEM 20130406 [235] Biology, NGS
GEMINI 4.6.6a, 0.13.1, 0.18.0 [236] Biology, Genomics, Genetics
GenBank Tools 20140130 [237] Biology, Genomics
GeneMark 2012.04 [238] Biology, Genomics, Metagenomics
GeneSeqer 20140226 [239] Biology, Genomics
Genewise 2.2.0 [240] Biology, Genomics, Annotation
Genome STRiP 2.00.1602 [241] Biology, genomics, NGS
GenomicConsensus 20160523 [242] Biology, Phylogenetics
GenomicTools 2.7.0 [243] Biology, NGS
GenomeTools 1.5.7 [244] Biology, Bioinformatics
GenSel 4.90 [245] Biology, Genetics
GET_HOMOLOGUES 20150529 [246] Biology, Genomics
GKNO 1.30.18 [247] Biology, NGS,
Git 1.8.2.1, 1.9.0 [248] Development, Revision Control
Glimmer 3.02 [249] Biology, Microbial Annotation
Globus 2.1.3 [250] Data Transfer
GLPK 4.55 [251] Biology, Genomics
Gmap 20150723, 20160501, 20160816 [252] Biology, Genomics
GNU Compilers 5.2.0 [253] Compilers, Programming
GnuPlot 4.6.0, 5.0.3 [254] Graphics, Plotting, Programming
Grace 5.1.22 [255] Graphics, plotting, 2D
GrADS 2.0.1 [256] Earth Science
GramCluster 1.3 [257] Biology, Sequencing
GRASS 7.0 [258] Geography
GraphViz 2.38.0 [259] Graphics, plotting, visualization
Gromacs 4.5.5, 4.6.5, 5.1.2 [260] Chemistry, Modeling, Simulation
GSNP 1.0 [261] Biology, Bioinformatics, NGS
GSL 1.15 [262] Library, Math, C++, C
Gsutil 4.15 [263] Cloud, Storage, Google
Gubbins 20150519, 20160421 [264] Biology, Phylogenetics, Genomics
GULP 4.0 [265] Material Science
HaMStR 13.2.2, 13.2.3, 13.2.4 [266] Biology, Genomics
HapCompass 0.7.7 [267] Biology, NGS, Genomics
HAPCUT 0.7 [268] Biology, Assembly
Hapsembler 2.21 [269] Biology, Genomics, NGS
HapTree 1.0 [270] Biology, Genomics, NGS
HDF4 4.2.11 [271] Library, Data
HDF5 1.8.9, 1.8.12, 1.8.15 [272] Library, Data
HISAT2 2.0.0b, 2.0.1b, 2.0.3b [273] Biology, Sequence Alignment, NGS
HMMER3 3.0, 3.1b1, 3.1b2 [274] Biology, Genomics
HMMSplicer 0.9.5 [275] Biology, Genomics
HOMER 4.2, 4.7, 4.8 [276] Biology, Genomics
HOOMD 1.3.3 [277] Chemistry
HTMLDoc 1.2.82 [278] Documentation, PDF, HTML
HTSeq 0.5.3p3, 0.6.1p1 [279] Biology, NGS
Hyb 20141126 [280] Biology, NGS, RNA-Seq
HyPhy 2.1.2.28, 2.2.6.1 [281] Biology, Phylogenetics
Hypre 1.10.0b, 2.8.0b [282] Library, Math, Physics
iAssembler 1.32 [283] Biology, Assembly
IBDNe 20150815 [284] Biology, NGS
iCommands 3.3.1 [285] Biology, iPlant, Data Tansfer
ICORN2 0.95 [286] Biology, Sequencing
IDBA-UD 1.0.9, 1.1.0, 1.1.1 [287] Biology, NGS
IDBA-MT 1.0 [288] Biology, NGS
IEP 3.6 [289] Programming, Python, Editor
IGB 8.4.1 [290] Biology, Genomics, NGS
iGTP 1.1 [291] Biology, Bioinformatics, Phylogenetics
illumiprocessor 20150803 [292] Biology, Sequencing
IM and IMa 20091217 [293] Biology, Population
IMa2 20120827 [294] Biology, Population
ImageJ 1.48 [295] Image manipulation
ImageMagick 6.8.8-9 [296] Image manipulation
IMOD 4.7.15 [297] 3D modeling, Image Reconstruction
Intel Compilers 2016.0.109 [298] Programming, Compilers
IOAPI 3.1 [299] Meteorology
Iprscan 4.8 [300] Biology, Genomics
IQ-TREE 1.3.11, 1.4.0, 1.4.2 [301] Biology, Phylogenetics
IRAP 0.8.1p7 [302] Biology, NGS, RNA-seq
ITK 4.3.1 [303] Biology, Genomics
ITK-SNAP 3.0.0 [304] Biology, Neuroscience, Imaging
JAGS 3.3.0 [305] Statistics
Java 1.7.0_79, 1.8.0_31 [306] Java Development Kit
Je 1.0. [307] Biology, NGS
Jellyfish 2.1.1 [308] Biology, NGS
JModelTest 2.1.1 [309] Biology, Phylogenetics, Genomics
Julia 0.3.11, 0.4.6 [310] Programming, Languages
KaKs 1.2 [311] Biology, Phylogenetics
Kent 20120524 [312] Biology, NGS
Khmer 1.1, 2.0 [313] Biology, NGS
KIM 1.7.2 [314] Library
KING 1.4, 1.9 [315] Biology, Genomics
KisSplice 2.4.0-p1 [316] Biology, NGS
Kallisto 0.42.3, 0.42.4 [317] Biology, NGS, RNA-Seq
KERAS 1.0.8 [318] Deep Learning
Kmer 1934 [319] Biology, NGS
KmerGenie 1.6741 [320] Biology, NGS, Utilities
Kraken 0.10.4b [321] Biology, Genomics, Phylogenetics
LAMMPS 28Oct12, 30Sep13, 28Jun14,15May15, 7Dec15, 30Jul16 [322] Molecular Dynamics Simulation
LAMP 2.5 [323] Biology, Genomics
Last 193, 247 [324] Biology, Sequence alignment
Lastz 1.03.02, 1.02.00 [325] Biology, NGS
LDhat 2.2a [326] Biology, Genomics
LIBSVM 3.12 [327] Machine Learning
LIGR 2.05 [328] Biology, Assembly
LFMM 1.4 [329] Biology, Genomics
LSC 0.3, 0.3.1 [330] Biology, NGS, Error correction
Loci 3.3 [331] Fluid Dynamics
LoRMA 0.3 [332] Biology, NGS
LS-DYNA 700, 711, 800 [333] Physics
Lumpy 0.2.1 [334] Biology, SNP
LZO 2.09 [335] Library, Data Compression
MACH 1.0.18 [336] Biology, Genomics
Mach2VCF 20150515 [337] Biology
M5tools 20121126 [338] Biology, Bioinformatics, Genomics
MACS 1.4.2, 2.1.1 [339] Biology, ChIP-Seq
mafft 7.215, 7.245, 7.294 [340] Biology, Multiple sequence alignment
Mash 1.1 [341] Biology, Genomics
Maker 2.25b, 2.31.6, 2.31.8 [342] Biology, Annotation, Genomics
MapSplice 2.1.7 [343] Biology, NGS, RNA-Seq
MAPminer 1.1 [344] Biology, Phylogenetics
MassMine 0.9.5, 0.10.0, 0.11.0 [345] Data Mining
Maq 0.7.1 [346] Biology, NGS
MARK 2.0.1 [347] Statistics
MarkerMiner 20150429, 20150511 [348] Biology, Genomics
MaSuRCA 2.3.2, 3.2.1 [349] Biology, NGS
Matlab 2012a, 2013a, 2014a [350] Math, Simulation, Programming
MATS 2.1.0, 3.0.8, 3.0.9 [351] BIology, NGS
Mauve 2.3.1 [352] Biology, NGS
MaxBin 2.1.1 [353] Biology, NGS
MCarts 1.0.2 [354] Biology, Genomics, Markov models
MCNP 5, 6b2, 6 [355] Physics
MCNPX 2.7.0, 2.7.0-i8 [356] Physics
MEGAN 5.10.3, 6.4.15 [357] Biology, NGS
Megraft 1.0.2 [358] Biology, Sequencing
Melting 4.3.1 [359] Biology, Genome, RNA, Folding
Meme 4.11.1, 4.11.2 [360] Biology, Motifs, Sequence analysis
Meraculous 2.0.5 [361] Biology, NGS
Mercurial 2.7 [362] Development, Revision Control
Merlin 1.1.2 [363] Biogolgy, SNP
Meta-Tissue 0.4 [364] Biology, Genetics
Metabin 1.0 [365] Biology, Metagenomics
MetaCluster 5.0b [366] Biology, Metagenomics
MetaCV 2.3.0 [367] Biology, NGS
METAL 20110325 [368] Biology, Genomics
MetAMOS 1.5.0rc4-20140827 [369] Biology, Bioinformatics, Genomics, Assembly
Metassembler 1.5 [370] Biology, Genomics
MetaVelvet 1.2.01 [371] Biology, NGS
Metaxa2 2.0.2, 2.1.1 [372] Biology, NGS
MetaGeneMark 2012.04 [373] Biology, Genomics
Mfold 3.6 [374] Biology, Genomics
MGEScan 1.1 [375] Biology, Genomics
MHAP 1.6 [376] Biology, Sequencing
MIA 20130301 [377] Biology, NGS
MicrobeCensus 1.0.7 [378] Biology, NGS
MIDAS 20160830 [379] Biology, Phylogenetics
Midnight Commander 4.6.1 [380] Tools, Utilities
Migrate-n 3.3.0, 3.6.6, 3.6.11 [381] Biology, Population
Minced 0.2.0 [382] Biology, Genomics
Minimac 2-20140915, 3-20151015 [383] Biology, Genomics
mira 3.9.18, 4.0.rc1, 4.0.2 [384] Biology, NGS
MISO 0.4.9, 0.5.2, 0.5.3 [385] Biology, NGS
MMSEQ 1.0.8 [386] Biology, NGS
MSMBuilder 2.5.1 [387] Molecular Dynamics
MOABS 1.2.9, 1.3.2, 1.3.4 [388] Biology, NGS, Genomics
Modeller 9.11, 9.13, 9.14 [389] Biology, Modeling
Molden 5.0 [390] Molecular, electronic structure
MolPro 2012.1p22 [391] Quantum Chemistry, Ab Initio
mosaik 2.1.33, 2.2.3 [392] Biology,NGS
Mothur 1.36.1, 1.37.0, 1.38.1 [393] Biology, Microbial Ecology
MOTU 1.1 [394] Biology, Bioinformatics, Genomics
MPE2 2.4.9b [395] MPI
MP-EST 1.4, 1.5 [396] Biology, Phylogenetics
mpiP 3.4.1 [397] Parallel Computing
MrBayes 3.2.1, 3.2.4, 3.2.5 [398] Biology, Phylogenetics
MRIcron 201306 [399] Biology, MRI, Imaging
MUMmer 3.23 [400] Biology, Genomics
MUSCLE 3.8.31 [401] Biology, Genomics
MuTect 1.1.4, 1.1.7 [402] Biology, Genomics
MutSig 1.4 [403] Biology, Genomics
MZMine 2.19, 2.20, 2.21 [404] Biology, Spectroscopy
NAMD 2.9, 2.11 [405] Simulation, Chemistry, Biology
Nanocorrect 20150727 [406] Biology, NGS
Nanopolish 20150904 [407] Biology
Nbody 6 [408] Astronomy
NCBI C++ Toolkit 12.0.0 [409] Biology, C++, Development
NCL 6.1.2, 6.3.0 [410] Atmosphere Science
NCO 4.2.1, 4.4.3 [411] Data exchange tools
Ncview 2.1.2 [412] Data visualization
NetCDF 3.4.2, 4.2, 4.3 [413] Data exchange, Tools
NEURON 7.4 [414] Biology, Neuroscience
Newbler 2.7, 2.8, 2.9 [415] Biology, NGS
Newick utils 1.6 [416] Biology, Phylogenetics
Nextallele 20140718 [417] Biology, Genomics
Nexus NCL 2.1.18 [418] Biology, Phylogenetics, Library
ngsCAT 0.1 [419] Biology, Bioinformatics, NGS
ngsTools 20150816 [420] Biology, NGS
NGSUtils 20130722, 20150206 [421] Biology, NGS
Nipype 0.10.0 [422] Biology, Bioinformatics, Neuroscience, Imaging
NMRPipe 7.9 [423] Biology, Biochemistry
Novoalign 2.08.02, 3.00.02 [424] Biology, NGS
NWChem 6.5, 6.6 [425] Chemistry
NxTrim 0.4.1 [426] Biology, Bioinformatics, NGS
Oases 0.2.08 [427] Biology, NGS
Olego 1.1.2, 1.1.5, 1.1.6 [428] Biology, NGS, RNA-Seq
OCaml 4.02.3 [429] Programming Languages, Scripting, Development
Octave 3.6.4 [430] Numerical Computation
Oncotator 1.5.2.0, 1.5.3.0, 1.8.0.0 [431] Biology, Genomics
OpenBabel 2.3.2 [432] Biology, Chemistry
OpenCL 1.1 [433] Programming, Library
OpenCV 2.4.8 [434] Computervision
OpenFOAM 2.1.1, 3.0.1, 4.0 [435] Fluid Dynamics
OpenMM 6.2.0 [436] Quantum Chemistry
Orange3 3.3.6 [437] Data Mining, Visualization
OrthoFinder 0.2.5, 0.6.0, 1.0.2 [438] Biology, Genomics
OrthoMCL 2.0.2, 2.0.3, 2.0.7 [439] Biology, Genomics
p4vasp 0.3.29 [440] Molecular, Electronic Structure
Pacbio 2.2.0, 2.3.0p5 [441] Biology, Bioinformatics, NGS
Package-GFE 20150701 [442] Biology, Genomics
PALES 122 [443] Physics
PAML 4.7, 4.8a, 4.9a [444] Biology, Phylogenetics
Pandaseq 20140808, 20150627 [445] Biology, Bioinformatics, NGS, Sequencing
PAPI 5.1.0.2 [446] Software, Computing
Parallel 20150122 [447] Programming, Languages
ParaView 4.1.0, 4.2.0, 4.3.0 [448] Data Analysis
Parsimonator 1.0.2 [449] Biology, Bioinformatics
PartitionFinder 1.0.1, 1.1.1 [450] Biology, Phylogenetics, Evolution
Parflow v615 [451] Ecology, Modeling
PASA 1.5, 2.0-r20150209 [452] Biology, Genomics
PASTA 20160616 [453] Biology, Sequence alignment,
PAUP 4.0b10, 4.1a147 [454] Biology, Phylogenetics
PAUDA 1.0.1 [455] Biology, Bioinformatics, Sequence alignment
PBalign 20160921 [456] Biology, Bioinformatics
PBCore 20151201 [457] Biology, Bioinformatics
PBCommand 20151203 [458] Biology, Library
PBJelly 14.7.14, 15.2.20, 15.8.24 [459] Biology, Bioinformatics
pbsdrmaa 1.0.17 [460] Libraries, Torque
p4est 1.1 [461] Library
pbsmrtpipe 20151202 [462] Biology
PeakSplitter 1.0 [463] Biology, Chip-Seq
PEAR 0.9.2, 0.9.6 [464] Biology, NGS
PDT 3.18, 3.20, 3.22 [465] Programming, Profiler
Perl 5.16.0 [466] Programming, Language
PerM 0.4.0 [467] Biology, NGS
PETSc 2.3, 3.3 [468] Math, Numerical solvers
PGDSpider 2.0.9.0 [469] Biology, NGS
Phenix 1.8.1069, 1.10.2155 [470] Crystallography
PHYLDOG 20130418 [471] Biology, Genomics, Phylogenetics
Phyluce 20140427, 20151103, 20160715 [472] Biology, Phylogenetics
PfamScan 1.3 [473] Biology, Genomics
PHITS 2.52, 2.76. 2.82 [474] Physics
PIPE-CLIP 1.1.0 [475] Biology, NGS
Pipits 1.3.6 [476] Biology, Sequencing
Phonopy 1.9.2 [477] Chemistry
PHYLIP 3.696 [478] Biology, Phylogenetics
PhyloBayes 3.3f, 1.4f MPI [479] Biology, Phylogenetics
PhyloNet 3.5.7 [480] Biology, Phylogenetics
Phylosift 1.1 [481] Biology, Genomics, Phylogenetics, Taxonomy
PhyML 3.0, 3.1 [482] Biology, Phylogenetics
Picard 1.72, 1.80, 2.0.1 [483] Biology, NGS
PICRUSt 1.0.0 [484] Biology, Phylogenetics
Piranha 1.2.1 [485] Biology, Phylogenetics
PLAST 1.0 [486] Biology, Bioinformatics
Platypus 0.8.1 [487] Biology, NGS
Plink 1.07, 1.90b3, 1.90b3.39 [488] Biology, GWAS
PLINKSEQ 0.10 [489] Biology, Genomics
PluMiST 1.1 [490] Biology, Phylogenetics, Genomics
PolyPhen 2.2.2.r405b [491] Biology, Genomics
Poretools 0.5.0 [492] Biology, Sequencing
POV-Ray 3.7 [493] 3D, Graphics
Prank 20150803 [494] Biology, Bioinformatics, Alignment
Preseq 0.0.4 [495] Biology, NGS
PRICE 1.2 [496] Biology, NGS
Primer3 2.3.4 [497] Biology, Genomics
PRIMUS 1.8.0 [498] Biology, Phylogenetics
PRINSEQ 0.20.4 [499] Biology, Sequencing
Prodigal 2.6.3 [500] Biology, Genomics
ProfessAtQE 2014 [501] Material Science, Molecular Dynamics
Prokka 1.10, 1.11 [502] Biology, Genomics, Bioinformatics, Assembly
ProBABEL 0.4.2, 0.4.3, 0.4.5 [503] Biology, Genomics, GWAS
Probalign 1.4 [504] Biology, Genomics
Proovread 1.03rcl [505] Biology, Genomics, NGS
Proteinortho 4.26, 5.11 [506] Biology, Genomics
PROVEAN 1.1.5 [507] Biology, Genomics
PyHDF 0.9.0 [508] Library, HDF4
Python 2.7.6, 3.5.0 [509] Biology, Genomics, NGS
Pyfasta 0.5.2 [510] Biology, Phylogenetics
Pyrad 3.0.63 [511] Biology, Sequencing Alignment, Assembly
QDD 3.1.2 [512] Programming, scripting, language
QIIME 1.5.0 [513] Biology, Ecology
QT 4.8.3 [514] Computer Science
QUAST 2.3 [515] Biology, NGS
Quake 0.3 [516] Biology, Sequencing
Quantas 1.0.4, 1.0.8 [517] Biology, Bioinformatics, NGS
QualiMap 2.1.1 [518] Biology, Sequence alignment
Quickquartet 1.0.0 [519] Biology, Phylogenetics
R Rmpi/3.3.1, 3.2.0, 3.3.0 [520] Statistics, Programming
R2R 1.0.4 [521] Biology, RNA
R8S 1.71, 1.8 [522] Biology, Evolution
RADICAL 0.2 [523] Biology, Phylogenetics, Genomics
Rascaf 1.0.2 [524] Biology, RNA-Seq
RAxML 8.1.23, 8.2.2, 8.2.3 [525] Biology, Phylogenetics
Ray 2.3.1 [526] Biology, Genomics, NGS
REAGO 1.1 [527] Biology, Assembly
REAPR 1.0.18 [528] Biology, Bioinformatics, Assembly
RELION 1.4 [529] Biology, Bioinformatics
RepeatExplorer 20150506 [530] Biology, Genomics
RepeatMasker 3.3.0 [531] Biology, Genomics
RepeatModeler 1.0.8 [532] Biology, Bioinformatics
Reptile 1.1 [533] Biology, NGS, error correction
RevBayes 1.0.0 [534] Biology, Phylogenetics
riboPicker 0.4.3 [535] Biology, Sequence
RNAhybrid 2.1.1 [536] Biology, Genomics
rRNASelector 1.0.0 [537] Biology, Sequencing
rnaQUAST 1.2.0 [538] Biology, NGS, Sequencing
ROOT 6.0 [539] Data Analysis
Roary 3.4.1 [540] Biology, Genomics
Rosetta 2014wk4 [541] Biology, Structure, Modelling
RSEG 0.4.8 [542] Biology, NGS
RSEM 1.2.19, 1.2.28, 1.2.29 [543] Biology, NGS, RNA-Seq
RSeQC 2.3.7, 2.6.2 [544] Biology, NGS, RNA-Seq
RStudio 0.99.902, 0.99.903 [545] R, Statistics, Programming
Ruby 1.9.3-p0 [546] Programming, Scripting, Language
Sailfish 0.6.3 [547] Biology, NGS, RNA-Seq
Salmon 0.6.0 [548] Biology, RNA-seq
Sambamba 0.5.0-dev, 0.5.10, 0.6.3 [549] Biology, NGS
Samstat 1.08 [550] Biology, NGS, Bioinformatics, Sequencing
Samblaster 0.1.14 [551] Biology, NGS
samtools 1.1, 1.2, 1.3.1 [552] Biology, NGS
SAS 9.3 [553] Statistics, Graphing
SATe 2.2.7 [554] Biology, Phylogenetics
Scala 2.11.5 [555] Programming, Language
Scalablast 2.4.53 [556] Biology, Genomics
Scalpel 0.1.1 [557] Biology, NGS
Shannon 20160211 [558] Biology, RNA-Seq
SHAPEIT 2.5.5 [559] Biology, SNP
Sharcgs 1.2.11 [560] Biology, NGS, Assembly
SHEsisPlus 1.0 [561] Biology, Phylogenetics
shustring 2.6 [562] Biology, Sequencing
SCons 2.3.0 [563] Programming
SCRATCH1D 1.0 [564] Biology, Genomics
Scythe 0.991 [565] Biology, NGS
SDT 1.2 [566] Biology, Sequencing
Segemehl 0.1.9 [567] Biology, NGS, Mapper
SEPP 1.0, 3.0 [568] Biology, Phylogenetics, HMM
SGA 0.10.14 [569] Biology, Assembly
Seq-Gen 1.3.3 [570] Biology, Phylogenetics
SeqPrep 0.5 [571] Biology, NGS
Seqmagick 20150923 [572] Biology, Phylogenetics
SeqMap 1.0.13 [573] Biology, NGS
Seqtk 20140729 [574] Biology, NGS
SEQuel 1.0.1 [575] Biology, NGS
SeqyClean 1.8.10 [576] Biology, NGS, Bioinformatics
ShoRAH 20131204 [577] Biology, NGS, quality filter
SHRiMP 2.2.3 [578] Biology, NGS
SICER 1.1 [579] Biology, ChIP-Seq
Sickle 1.200, 1.33 [580] Biology, NGS, quality filter
Siesta 2.0.2,3.1 [581] Simulation, Physics, Ab Initio
SIFT 4.0.3b [582] Biology, Genomics
SignalP 4.1c [583] Biology, NGS
Silo 4.7 [584] Library, Data
SIPeS 2.0 [585] Biology, Bioinformatics, ChIP-Seq
Slicer 4.3.1 [586] Biology, Imaging
SMALT 0.7.6 [587] Biology, NGS
Snap 20100728 [588] Biology, Genomics
SNAPE-pooled 20130407 [589] Biology, SNP
SNeP 1.1 [590] Biology, Phylogenics
SnpEff 4.1i, 4.2, 4.3 [591] Biology, NGS, Genomics
SNPhylo 20140701 [592] Bilogy, Phylogenetics
SNP-sites 2.0.3 [593] Biology, SNP
Snippy 20160419 [594] Biology, Phylogenetics
SOAPdenovo 1.05 [595] Biology, NGS
SOAPdenovo-Trans 1.01, 1.03 [596] Biology, NGS
SOAPsplice 1.10 [597] Biology, NGS
SortMeRNA 2.1 [598] Biology, Sequencing, NGS
SparCC 201402 [599] Microbial Ecology
Spades 3.7.1, 3.8.0, 3.9.0 [600] Biology, NGS
Spanki 0.4.1, 0.4.3, 0.5.0 [601] Biology, NGS, RNA-Seq
SPARTA+ 2.60 [602] Chemistry
Spidey 20150922 [603] Biology, Genomics
SPIMAP 1.1 [604] Biology, Phylogenetics
SpliceTrap 0.90.5 [605] Biology, NGS, RNA-Seq
SPM 8 [606] Biology, Statistics, Neurology, Imaging
Sputnik 1.0 [607] Biology, Genomics
SQLite 3.8.8.2 [608] Database
SQL_Developer 4.1.2 [609] Programming, Oracle, Sql
SRA 2.1.10 [610] biology, NGS
SSPACE 2.0, 3.0 [611] Biology, NGS
SST-Core 6.0.0 [612] MPI
SSR_pipeline 0.951 [613] Bilogy, DNA Sequencing
Stacks 1.21, 1.24, 1.35 [614] Biology, Genomics, NGS
Staden 1.14.6 [615] Biology, Sequencing
STAR 2.4.0j, 2.5.1b [616] Biology, NGS, Alignment
STAR-CCM+ 8.06 [617] Mechanical Engineering
Stata 10.1, 13 [618] Statistics, Data analysis
Stringtie 1.0.0, 1.1.2, 1.2.1 [619] Biology, NGS, Alignment
Structure 2.3.3, 2.3.4 [620] Biology, Population
Subread 1.5.0-p1, 1.5.1 [621] Biology, Sequencing, SNP
SUNDIALS 2.3.0, 2.5.0 [622] Numerical Solver
SVDetect 0.8b [623] Biology, NGS, SNP
swak4Foam 2.x [624] Fluid Dynamics
swarm 1.2.11 [625] Data Analysis
SWEEP 20160722 [626] Biology, SNP
Swig 2.0.9 [627] Programming, C, C++, Python
SwitchSeq 20140907 [628] Biology, NGS
Syzygy 1.2.7 [629] Biology, Genomics
TetGen 1.5.0 [630] Tetrahedral Meshes 3D
tapir 20160825 [631] Biology, Phylogenetics
TASSEL 5.0, 5.2.29 [632] Biology, Genomics
TAU 2.21.4, 2.23, 2.24, 2.52 [633] Profiling, Tracing, Programming
taxMap 0.1 [634] Biology, Phylogenetics, Taxonomy
T-Coffee 9.03.r1318 [635] Biology, Genomics, Multiple Alignment
TensorFlow 0.10.0 [636] Library, Math
TESS 2.3.1 [637] Biology, Genomics, Markov
tgicl 2.1 [638] Biology, sequencing, clustering
Tmux 2.0 [639] GNU, Terminal Multiplexer
TomoPy 0.0.3 [640] Biology, Neuroimaging
Tophat 1.4.1, 2.0.13, 2.1.0 [641] Biology, NGS
Torch 20160704 [642] Lua
Totalview 8.12.0 [643] Computer Science
TPP 4.7.0 [644] Bioinformatics, MassSpec
TrackTools 2011 [645] Bioinformatics
TrackVis 0.5.2.2 [646] Biology, Spectroscopy
Tracula 5.3.2014_05_26 [647] Biology, Bioinformatics, Neuroscience, Imaging
TraitRate 1.1 [648] Biology, Evolution
Trans-ABySS 1.5.4 [649] Biology, Phylogenetics
TransDecoder 20140704, 2.0.1, 3.0.0 [650] Biology, NGS
Transrate 1.0.1 [651] Biology, Assembly
TraCeR 20160519 [652] Biology, Bioinformatics
TreeCorr 3.2.3 [653] Physics
TreeFix 1.1.7, 1.1.10 [654] Biology, Phylogenetics
TreeMix 1.12 [655] Biology, Phylogenetics
TreePL 20150305 [656] Biology, Phylogenetics
TriMetAss 1.1 [657] Biology, Bioinformatics, NGS
TRF 4.04 [658] Biology, Genomics
Trilinos 11.4.1, 11.8.1 [659] Math Algorithm
trimAl 1.2 [660] Biology, Genomics, Sequence Alignment
Trim Galore 0.2.8, 0.4.1 [661] Biology, NGS
Trimmomatic 0.32, 0.33, 0.36 [662] Biology, NGS
Trinity r20151015-2.1.1, r20160329-2.2.0 [663] Biology, NGS, RNA-Seq
Trinotate 2.0.1, 3.0.1 [664] Biology
TRNAscan-SE 1.23 [665] Biology, NGS, Bioinformatics
Twinscan 4.1.2 [666] Biology, Genomics
usearch 7.0.1001-64, 8.0.1517 [667] Biology, Sequence analysis
UDUNITS 2.2.17 [668] Library, Units, Programming
UNAFold 3.8 [669] Biology, Genome, RNA, Folding
UProC 1.2.0 [670] Biology, Genomics
Valgrind 3.9.0 [671] Computer Science
VarDictJava 20160521 [672] Biology, NGS
VarScan 2.3.6 [673] Biology, NGS, Genomics
VASP 5.3.2, 5.3.3, 5.3.5, 5.4.1 [674] Quantum Chemistry, Ab Initio
VAST-TOOLS 20150506 [675] Biology, NGS, RNA-Seq
VCFLib 20141119, 20150313 [676] Biology, NGS, Genomics
VCFtools 0.1.12a, 0.1.12b, 0.1.14 [677] Biology, SNPs
velvet 1.2.06, 1.2.07, 1.2.10 [678] Biology, Genomics, NGS
VEP 74, 83 [679] Biology, NGS
VICUNA 1.3 [680] Biology, Assembly
ViennaRNA 2.2.6 [681] Biology, RNA-seq
Vim 7.4.5 [682] Programming, Scripting, Language
vmd 1.9.1 [683] Biology, Visualization
VSearch 20151022 [684] Biology, NGS
VT 20140903, 20160129 [685] Biology, Genomics
VTK 6.1.0 [686] Visualization, Graphics
V-Phaser2 02112013 [687] Biology, Phylogenetics
Wannier90 1.2, 2.0.0 [688] Computational Physics
WebLogo 3.3 [689] Biology, Genomics
WDSSII 1 [690] Meteorology
WIEN2k 12.1 [691] Material Science, Chemistry
Wgs or Celera 8.2, 8.3rc1, 8.3rc1.r4638 [692] Biology, NGS
wublast 2.0 [693] Biology, Sequence Alignment
YAHA 0.1.82 [694] Biology NGS
XCrySDen 1.5.60 [695] Computational Material Science
Yambo 3.3.0 [696] Physics
YASM 1.3.0 [697] Computer Science
Yasra 2.32 [698] Biology, NGS
Zagros 1.0.0 [699] Biology, NGS
Zeo++ 0.2.2 [700] Chemistry
Zorro 2.2 [701] 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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