Difference between revisions of "Installed Software"

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Line 631: Line 631:
 
| [[MACS]] || 1.4.2 || [http://liulab.dfci.harvard.edu/MACS/]||Biology, ChIP-Seq
 
| [[MACS]] || 1.4.2 || [http://liulab.dfci.harvard.edu/MACS/]||Biology, ChIP-Seq
 
|-
 
|-
| [[mafft]] || 7.215, 7.245, 7.294 || [http://mafft.cbrc.jp/alignment/software/]||Biology, Multiple sequence alignment
+
| [[mafft]] || 7.215, 7.245, 7.294 || [http://mafft.cbrc.jp/alignment/software/] || Biology, Multiple sequence alignment
 +
|-
 +
| [[Mash]] || 1.1 || [http://mash.readthedocs.io/en/latest/] || Biology, Genomics
 
|-
 
|-
 
| [[Maker]] || 2.25b, 2.31.6, 2.31.8 || [http://www.yandell-lab.org/software/maker.html] || Biology, Annotation, Genomics
 
| [[Maker]] || 2.25b, 2.31.6, 2.31.8 || [http://www.yandell-lab.org/software/maker.html] || Biology, Annotation, Genomics

Revision as of 15:22, 13 June 2016

  • Last updated on 2016-06-13.
  • 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, 1.3.0 [5] Biology, Bioinformatics, Genomics, NGS
AEGeAn 0.14.0 [6] Biology, Genomics
AFNI 2013_11_24, 2016_0_19 [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
AMAS 0.98 [12] Biology, Sequence Alignment
AMOS 3.1.0 [13] Biology, Genomics, NGS
AMPHORA2 20140305 [14] Biology, Phylogenetics
Anvio 1.2.3 [15] Biology, Microbial 'omics
ANNOVAR 20120621, 20150322 [16] Biology, Genomics
AStalavista 3.2 [17] Biology, NGS, RNA-Seq, Genomics
ASTRID 20150807 [18] Biology, Genomics
Atlas 3.10.1, 3.11.17 [19] Library, Math
Amuse 6.0, 10.0 [20] Astrophysics
ANGSD 20150306, 20150909 [21] Biology, NGS
Affymetrix Power Tools 1.15.0, 1.18.0 [22] Biology, Genomics, Microarray
ARC 20140312 [23] Biology, NGS
Armadillo 6.200.3 [24] Library, C++ , Math
Astral 4.7.8, 4.7.9, 4.10.5 [25] Biology, Bioinformatics, NGS, Phylogenetics
AtomEye 3 [26] Material Science
ATRAM 20140624 [27] Biology, NGS
Augustus 2.6, 3.2.1 [28] Biology, NGS
Auto3DEM 4.05.1, 4.05.2 [29] Image Reconstruction
BamBam 1.0 [30] Biology, NGS
BAMM 2.5.0 [31] Biology, Phylogenetics
Bam-readcount 20150216 [32] Biology, NGS
Bamstats 20140602 [33] Biology, NGS
Bamtools 2.1.1 [34] Biology, NGS
BamUtil 1.0.2 [35] Biology, NGS
Bam-Readcount 20150616 [36]] Biology, Genomics
BAPS 6.0 [37] Biology, Populaton genetics
Barrnap 0.7 [38] Biology, RNA-Seq
Basemount 0.1.2.464 [39] Biology, DNA Sequencing
BayArea 1.0.2 [40] Biology
BayesRate 1.3.43 [41] Biology, Phylogenetics
Bbcp 12.08.17.00.0 [42] Network file transfer
Bcbio-nextgen 0.8.7 [43] Biology, NGS
Bcftools 1.0, 1.2 [44] Biology, Genomics, NGS
Bcl2fastq 2.16 [45] Biology, NGS, Illumina
BEAGLE 3.2.2, 4.0 [46] Biology, Genetics, Genotyping
BEAST 1.7.5, 1.8.1, 2.3.2 [47] Biology, Phylogenetics
Bedops 2.4.2 [48] Biology, Bioinformatics, Sequence, NGS
BEDTools 2.17.0, 2.23.0, 2.24.0 [49] Biology, NGS
BEST 2.3.1 [50] Biology, Phylogenetics
BETA 1.0.5 [51] Biology, NGS
BFAST 0.7.0 [52] Biology, NGS
Bismark 0.7.4, 0.7.7, 0.13.0 [53] Biology, NGS, Methylation
BinPacker 1.0 [54] Biology, RNA-Seq, Sequence Assembly
Bioconductor Latest [55] Biology, R, Statistics
BioPerl 1.006901 [56] Biology, Perl
BioPython 1.59 [57] Biology, Python
BLASR 20130815 [58] Biology, NGS
NCBI BLAST 2.2.27, 2.2.28, 2.2.29 [59] Biology, Sequence alignment
Blast2go 2.5.0-20120705 [60] Biology, Annotation
BLAT 20120524 [61] Biology, Sequence alignment
Blender 2.63 [62] Graphics
BoltzTraP 1.2.5 [63] Physics
Boost 1.49.0, 1.53.0, 1.54.0 [64] C++, Library
Bowtie 0.12.9, 1.0.0, 1.1.1 [65] Biology, NGS
Bowtie2 2.2.5, 2.2.6, 2.2.8 [66] Biology, NGS
BPP 1.9.0, 2.2, 3.2 [67] Biology, Phylogenetics
BRANCH 1.8.1 [68] Biology, NGS, Mapping
BRATNextGen 20150505 [69] Biology, Genomics
BRIG 0.95 [70] Biology, Genomics
Bsoft 1.9.1 [71] Biology, Image Analysis
Bsmap 2.74, 2.87 [72] Biology, NGS, Methylation
BUCKy 1.4.4 [73] Biology, Genomics
Busco 1.1b1 [74] Biology, Genomics
Bwa 0.6.1, 0.7.11, 0.7.12 [75] Biology, NGS
BXH_XCEDE_tools 1.11.1 [76] Biology, Bioinformatics
Camino 20140723 [77] Biology, Neuroscience, Imaging
Canu 1.0, 1.1 [78] Biology, Sequencing
CAP3 20120705 [79] Biology, Sequence Assembly
CASAVA 1.8.2 [80] Biology, NGS
CD-HIT 4.6, 4.6.4 [81] Biology, Genomics
CDO 1.6.1, 1.7.2rc5 [82] Climate
CEAS 1.0.2 [83] Biology, Genomics
CellProfiler 2.0 [84] Biology, Image Analysis
CFITSIO 3.370 [85] Library, C
CGATools 1.6.0.42 [86] Biology, NGS
Charmm 36a3 [87] Simulation, Chemistry
Chartdirector 5.1.0 [88] Graphics
CheckM 1.0.4 [89] Biology, Genomics
Chimera 1.7 [90] Biology, Modeling
ChromEvol 2.0 [91] Biology, Phylogenetics
CIMS 4.1.2 [92] Biology, Genomics
Circos 0.63-pre11, 0.69-2 [93] Biology, Visualization
CisGenome 2.0 [94] Biology, Genomics, Peak Calling
Clann 3.2.3 [95] Biology, Phylogenetics
CLARK 1.2.2-b [96] Biology, Genomics
CLHEP 2.2.0.1 [97] High Energy Physics
CLIPper 1.0 [98] Biology, Sequencing
CLIPSeqTools 0.1.7 [99] Biology, Sequencing
ClonalFrame 1.1, 1.2 [100] Biology, Genomics, NGS
ClonalFrameML 1.25 [101] Biology, Genomics, NGS
ClustalW 2.1 [102] Biology, Genomics
Cluster3 1.52 [103] Biology, Genomics
Clview 20130402 [104] Biology, Genomics
ClustalO 1.2.0 [105] Biology, Genomics
ClusterFinder 313 [106] Biology, Metabolomics
CMake 2.8.8, 2.9.12.1, 3.1.0 [107] Programming, Build System
CMWP 140518 [108] Biology, Genomics
CNVSeq 20110715 [109] Biology, NGS
Cobrapy 0.3.2 [110] Biology, Metabolomics, Modeling
Coevol 1.3c, 1.4b [111] Biology, Phylogenetics
CoMap 1.4.1 [112] Biology, Genomics
CONCOCT 0.3.1 [113] Biology, Genomics
CoNIFER 0.2.2 [114] Biology, Genomics
Consed 23.0 [115] Biology, Genomics
Coreutils 8.23 [116] GNU Utilities, Computer Science
covNMR 2014 [117] Biochemistry
CPLEX 12.6.5 [118] Optimizer
CUDA 4.2, 5.5 [119] Programming, Graphics
CrossMap 0.2.3 [120] Biology, Genomics
Crux 1.40 [121] Biology, Mass-Spectrometry
Cufflinks 1.3.0, 2.0.2, 2.2.1 [122] Biology, NGS
Cutadapt 1.1, 1.7.1, 1.8.1 [123] Biology, NGS
CUTE 20160116 [124] Cosmology
DAKOTA 5.4.0 [125] Computational Science
DaPars 0.9.0 [126] Biology, NGS, RNA-Seq
DALIGNER 1.0 [127] Biology, Sequencing
Datamash 1.1.0 [128] Math
DCMTK 3.6.0 [129] Biology, Neuroscience, Imaging
DSSAT 4.5 [130] Biology
dDocent 20160425 [131] Biology
DDSCAT 7.3.0 [132] Astrophysics
DDT 4.1.0, 4.2.1 [133] Software
Dealii 8.3.0 [134] Library
DeconSeq 0.4.3 [135] Biology, Phylogenetics
Delft3D 3621 [136] Hydrodynamics, Physics
Desmond 3.0.3.1 [137] Simulation, Biology, Chemistry
DETONATE 1.9 [138] Biology, NGS
Dalton 2011 [139] Quantum Chemistry
Diamond 0.5.1 [140] Computational Biology, Genomics
Dibig Tools 1.0 [141] Bioinformatics, PBS, Torque, Jobs
DiffReps 1.55.4 [142] Biology, NGS, ChIP-Seq
Dindel 1.01 [143] Biology, NGS
DISCOVARdenovo 52488 [144] Biology, NGS
DIYABC 1.0.4.43b, 2.0.3 [145] Biology, Genomics
Dlpoly 4.03.4 [146] Simulation, Biology, Chemistry
Dlpoly-Classic 1.9 [147] Simulation, Biology, Chemistry
DNA Clust 3.0 [148] Biology, Genomics
Dock 6.5, 6.6, 6.7 [149] Chemistry, ligand binding prediction
DOT 2.0 [150] Biology, Bioinformatics, Docking
Doxygen 1.8.3.1 [151] Programming, Documentation
DSSP 2.2.1 [152] Biology, Molecular Dynamics
DTI-TK 2.3.1 [153] Biology, Neurology, Imaging
EA-Utils 1.1.2.537 [154] Biology, NGS
ECTools 20140311, 20141201 [155] Biology, Sequencing, Bioinformatics
EEGLAB 12.0.2.1b, 13.2.2b, 13.4.4b [156] Biology, Matlab
eGene-MVN 0.1 [157] Biology, Genetics
eigenMT 20160228 [158] Biology, Genetics
EIGENSOFT 4.2, 5.0.1, 6.0.1 [159] Biology, Population
emboss 6.5.7 [160] Biology, multi-tool suite
EMAN2 2.11 [161] Biology
EMIRGE 20130727 [162] Biology, NGS
Ensembl_Tools 80 [163] Biology, Bioinformatics
EPACTS 3.2.6 [164] Biology, Bioinformatics, Genomics
EPOCH 4.7.3 [165] Astronomy, CPPP
eQTLA 1.1 [166] Biology, Genomics
Eqtlbma 1.2.2 [167] Biology, Genotyping
Esmf 6.3.0rp1 [168] Climate
Espresso 5.0.1, 5.2.0, 5.2.1, 5.3.0 [169] Modeling, Physics
ESPRIT 201211 [170] Biology, NGS, Metagenomics
ETE2 2.1 [171] Biology, Phylogenetics
Eval 2.2.8 [172] Biology, Genomics, GUI
ExaBayes 1.2.1, 1.4.1 [173] Biology, Phylogenetics
ExaML 1.0.5, 1.0.12, 3.0.14, 3.0.17 [174] Biology, Phylogenetics
ExomeCNV 1.4 [175] Biology, NGS, Genomics
Exonerate 2.2.0 [176] Biology, Genomics
eXpress 1.3.1 [177] Biology, NGS
FALCON 20130305, 20160108 [178] Biology, Bioinformatics, NGS, Sequencing
FAR 2.15 [179] Biology, Genomics
FASTA 34.26.5, 36.3.6d [180] Biology, Genomics
FAST-iCLIP 0.9.1 [181] Biology, Sequencing
FastML 3.0 [182] Biology, Phylogenetics, ML
FastQC 0.10.1, 0.11.2, 0.11.4 [183] Biology, NGS
Fastq-tools 0.7, 0.8 [184] Biology, NGS
FastStructure 20150112 [185] Biology, Genomics
FastTree 2.1.7 [186] Biology, Phylogenetics
Fastx_toolkit 0.0.13.2 [187] Biology, NGS
Fathmm 20150225 [188] Biology, Genomics
fcGENE 1.0.7 [189] Biology, Genomics, SNP
Ferret 6.82 [190] Oceanography, Meteorology
FFmpeg 2.1.3, 2.8.3 [191] Multimedia, audio, video
FFTW 3.3.2, 3.3.3, 3.3.4 [192] Math, Library, C++
FLASH 1.2.10, 1.2.11 [193] Biology, Genomics, NGS
Flexbar 2.3 [194] Biology, Genomics, NGS
Fluent 14.5.7, 15.0.7, 16.0 [195] Simulation, Fluid Dynamics
FragGeneScan 1.16 [196] Biology, NGS, Genomics
FreeBayes 0.9.21, 1.0.1, 1.0.2 [197] Biology, NGS, SNP Calling
Freesurfer 5.2.0, 5.3.0 [198] Biology, Neurology, Imaging
FSL 5.0.2.2 [199] Biology, Neurology, Imaging
Galaxy latest [200] Biology, Chemistry, Other
GapFiller 1.11 [201] Biology, NGS
Garli 2.0, 2.01 [202] Biology, Phylogenetics
GAML 20150610 [203] Biology, NGS
GARM 0.7.4 [204] Biology, NGS
GASVPro 201310 [205] Biology, NGS, Genomics
GATE 7.0 [206] Data Analysis
GATK 1.6.9, 3.4.46, 3.5.0 [207] Biology, NGS
Gaussian G03, G09-A.02, G09-C.01 [208] Modeling, Computational Chemistry
Gblocks 0.91b [209] Genomics, Alignment tool
GCTA 1.24.7 [210] Biology, Genomics, SNP
GDAL 1.11.2 [211] Geospatial Data Modeling, Geospatial Library
Geant4 4.10 [212] Physics
GEM 20130406 [213] Biology, NGS
GEMINI 4.6.6a, 0.13.1, 0.18.0 [214] Biology, Genomics, Genetics
GenBank Tools 20140130 [215] Biology, Genomics
GeneMark 2012.04 [216] Biology, Genomics, Metagenomics
GeneSeqer 20140226 [217] Biology, Genomics
Genewise 2.2.0 [218] Biology, Genomics, Annotation
Genome STRiP 2.00.1602 [219] Biology, genomics, NGS
GenomicConsensus 20160523 [220] Biology, Phylogenetics
GenomicTools 2.7.0 [221] Biology, NGS
GenomeTools 1.5.7 [222] Biology, Bioinformatics
GenSel 4.90 [223] Biology, Genetics
GET_HOMOLOGUES 20150529 [224] Biology, Genomics
GKNO 1.30.18 [225] Biology, NGS,
Git 1.8.2.1, 1.9.0 [226] Development, Revision Control
Glimmer 3.02 [227] Biology, Microbial Annotation
Globus 2.1.3 [228] Data Transfer
GLPK 4.55 [229] Biology, Genomics
Gmap 20150612, 20150723, 20160501 [230] Biology, Genomics
GNU Compilers 5.2.0 [231] Compilers, Programming
GnuPlot 4.6.0, 5.0.3 [232] Graphics, Plotting, Programming
Grace 5.1.22 [233] Graphics, plotting, 2D
GrADS 2.0.1 [234] Earth Science
GramCluster 1.3 [235] Biology, Sequencing
GraphViz 2.38.0 [236] Graphics, plotting, visualization
Gromacs 4.5.5, 4.6.5 [237] Chemistry, Modeling, Simulation
GSNP 1.0 [238] Biology, Bioinformatics, NGS
GSL 1.15 [239] Library, Math, C++, C
Gsutil 4.15 [240] Cloud, Storage, Google
Gubbins 20150519, 20160421 [241] Biology, Phylogenetics, Genomics
GULP 4.0 [242] Material Science
HaMStR 13.2.2, 13.2.3, 13.2.4 [243] Biology, Genomics
HapCompass 0.7.7 [244] Biology, NGS, Genomics
HAPCUT 0.7 [245] Biology, Assembly
Hapsembler 2.21 [246] Biology, Genomics, NGS
HapTree 1.0 [247] Biology, Genomics, NGS
HDF4 4.2.11 [248] Library, Data
HDF5 1.8.9, 1.8.12, 1.8.15 [249] Library, Data
HISAT2 2.0.0b, 2.0.1b, 2.0.3b [250] Biology, Sequence Alignment, NGS
HMMER3 3.0, 3.1b1, 3.1b2 [251] Biology, Genomics
HMMSplicer 0.9.5 [252] Biology, Genomics
HOMER 4.2 [253] Biology, Genomics
HOOMD 1.3.3 [254] Chemistry
HTMLDoc 1.2.82 [255] Documentation, PDF, HTML
HTSeq 0.5.3p3, 0.6.1p1 [256] Biology, NGS
Hyb 20141126 [257] Biology, NGS, RNA-Seq
HyPhy 2.1.2.28, 2.2.6.1 [258] Biology, Phylogenetics
Hypre 1.10.0b, 2.8.0b [259] Library, Math, Physics
iAssembler 1.32 [260] Biology, Assembly
IBDNe 20150815 [261] Biology, NGS
ICORN2 0.95 [262] Biology, Sequencing
IDBA-UD 1.0.9, 1.1.0, 1.1.1 [263] Biology, NGS
IDBA-MT 1.0 [264] Biology, NGS
IEP 3.6 [265] Programming, Python, Editor
IGB 8.4.1 [266] Biology, Genomics, NGS
iGTP 1.1 [267] Biology, Bioinformatics, Phylogenetics
illumiprocessor 20150803 [268] Biology, Sequencing
IM and IMa 20091217 [269] Biology, Population
IMa2 20120827 [270] Biology, Population
ImageJ 1.48 [271] Image manipulation
ImageMagick 6.8.8-9 [272] Image manipulation
Intel Compilers 2016.0.109 [273] Programming, Compilers
IOAPI 3.1 [274] Meteorology
Iprscan 4.8 [275] Biology, Genomics
IQ-TREE 1.3.11, 1.4.0, 1.4.2 [276] Biology, Phylogenetics
ITK 4.3.1 [277] Biology, Genomics
ITK-SNAP 3.0.0 [278] Biology, Neuroscience, Imaging
JAGS 3.3.0 [279] Statistics
Java 1.6.0_31, 1.7.0_02, 1.8.0_31 [280] Java Development Kit
Je 1.0. [281] Biology, NGS
Jellyfish 2.1.1 [282] Biology, NGS
JModelTest 2.1.1 [283] Biology, Phylogenetics, Genomics
Julia 0.3.11 [284] Programming, Languages
KaKs 1.2 [285] Biology, Phylogenetics
Kent 20120524 [286] Biology, NGS
Khmer 1.1, 2.0 [287] Biology, NGS
KING 1.4, 1.9 [288] Biology, Genomics
Kallisto 0.42.3, 0.42.4 [289] Biology, NGS, RNA-Seq
Kmer 1934 [290] Biology, NGS
KmerGenie 1.6741 [291] Biology, NGS, Utilities
Kraken 0.10.4b [292] Biology, Genomics, Phylogenetics
LAMMPS 28Oct12, 30Sep13, 28Jun14,15May15, 7Dec15 [293] Molecular Dynamics Simulation
LAMP 2.5 [294] Biology, Genomics
Last 193, 247 [295] Biology, Sequence alignment
Lastz 1.03.02, 1.02.00 [296] Biology, NGS
LDhat 2.2a [297] Biology, Genomics
LIBSVM 3.12 [298] Machine Learning
LIGR 2.05 [299] Biology, Assembly
LFMM 1.4 [300] Biology, Genomics
LSC 0.3, 0.3.1 [301] Biology, NGS, Error correction
Loci 3.3 [302] Fluid Dynamics
LS-DYNA 700, 711, 800 [303] Physics
Lumpy 0.2.1 [304] Biology, SNP
LZO 2.09 [305] Library, Data Compression
MACH 1.0.18 [306] Biology, Genomics
Mach2VCF 20150515 [307] Biology
M5tools 20121126 [308] Biology, Bioinformatics, Genomics
MACS 1.4.2 [309] Biology, ChIP-Seq
mafft 7.215, 7.245, 7.294 [310] Biology, Multiple sequence alignment
Mash 1.1 [311] Biology, Genomics
Maker 2.25b, 2.31.6, 2.31.8 [312] Biology, Annotation, Genomics
MapSplice 2.1.7 [313] Biology, NGS, RNA-Seq
MAPminer 1.1 [314] Biology, Phylogenetics
MassMine 0.9.5, 0.10.0, 0.11.0 [315] Data Mining
Maq 0.7.1 [316] Biology, NGS
MARK 2.0.1 [317] Statistics
MarkerMiner 20150429, 20150511 [318] Biology, Genomics
MaSuRCA 2.3.2 [319] Biology, NGS
Matlab 2012a, 2013a, 2014a [320] Math, Simulation, Programming
MATS 2.1.0, 3.0.8, 3.0.9 [321] BIology, NGS
Mauve 2.3.1 [322] Biology, NGS
MaxBin 2.1.1 [323] Biology, NGS
MCarts 1.0.2 [324] Biology, Genomics, Markov models
MCNP 5, 6b2, 6 [325] Physics
MCNPX 2.7.0, 2.7.0-i8 [326] Physics
MEGAN 5.10.3 [327] Biology, NGS
Megraft 1.0.2 [328] Biology, Sequencing
Melting 4.3.1 [329] Biology, Genome, RNA, Folding
Meme 4.8.1 [330] Biology, Motifs, Sequence analysis
Meraculous 2.0.5 [331] Biology, NGS
Mercurial 2.7 [332] Development, Revision Control
Merlin 1.1.2 [333] Biogolgy, SNP
Meta-Tissue 0.4 [334] Biology, Genetics
Metabin 1.0 [335] Biology, Metagenomics
MetaCluster 5.0b [336] Biology, Metagenomics
MetaCV 2.3.0 [337] Biology, NGS
METAL 20110325 [338] Biology, Genomics
MetAMOS 1.5.0rc4-20140827 [339] Biology, Bioinformatics, Genomics, Assembly
Metassembler 1.5 [340] Biology, Genomics
MetaVelvet 1.2.01 [341] Biology, NGS
Metaxa2 2.0.2, 2.1.1 [342] Biology, NGS
MetaGeneMark 2012.04 [343] Biology, Genomics
Mfold 3.6 [344] Biology, Genomics
MGEScan 1.1 [345] Biology, Genomics
MHAP 1.6 [346] Biology, Sequencing
MIA 20130301 [347] Biology, NGS
Midnight Commander 4.6.1 [348] Tools, Utilities
Migrate-n 3.3.0, 3.6.6 [349] Biology, Population
Minced 0.2.0 [350] Biology, Genomics
Minimac 2-20140915, 3-20151015 [351] Biology, Genomics
mira 3.9.18, 4.0.rc1, 4.0.2 [352] Biology, NGS
MISO 0.4.9, 0.5.2, 0.5.3 [353] Biology, NGS
MMSEQ 1.0.8 [354] Biology, NGS
MSMBuilder 2.5.1 [355] Molecular Dynamics
MOABS 1.2.9, 1.3.2, 1.3.4 [356] Biology, NGS, Genomics
Modeller 9.11, 9.13, 9.14 [357] Biology, Modeling
Molden 5.0 [358] Molecular, electronic structure
MolPro 2012.1p22 [359] Quantum Chemistry, Ab Initio
mosaik 2.1.33, 2.2.3 [360] Biology,NGS
Mothur 1.31.2, 1.36.1, 1.37.0 [361] Biology, Microbial Ecology
MOTU 1.1 [362] Biology, Bioinformatics, Genomics
MP-EST 1.4, 1.5 [363] Biology, Phylogenetics
mpiP 3.4.1 [364] Parallel Computing
MrBayes 3.2.1, 3.2.4, 3.2.5 [365] Biology, Phylogenetics
MRIcron 201306 [366] Biology, MRI, Imaging
MUMmer 3.23 [367] Biology, Genomics
MUSCLE 3.8.31 [368] Biology, Genomics
MuTect 1.1.4, 1.1.7 [369] Biology, Genomics
MutSig 1.4 [370] Biology, Genomics
MZMine 2.15, 2.17, 2.19 [371] Biology, Spectroscopy
NAMD 2.9 [372] Simulation, Chemistry, Biology
Nanocorrect 20150727 [373] Biology, NGS
Nanopolish 20150904 [374] Biology
Nbody 6 [375] Astronomy
NCBI C++ Toolkit 12.0.0 [376] Biology, C++, Development
NCL 6.1.2, 6.3.0 [377] Atmosphere Science
NCO 4.2.1, 4.4.3 [378] Data exchange tools
Ncview 2.1.2 [379] Data visualization
NetCDF 3.4.2, 4.2, 4.3 [380] Data exchange, Tools
Newbler 2.7, 2.8, 2.9 [381] Biology, NGS
Newick utils 1.6 [382] Biology, Phylogenetics
Nextallele 20140718 [383] Biology, Genomics
Nexus NCL 2.1.18 [384] Biology, Phylogenetics, Library
ngsCAT 0.1 [385] Biology, Bioinformatics, NGS
ngsTools 20150816 [386] Biology, NGS
NGSUtils 20130722, 20150206 [387] Biology, NGS
Nipype 0.10.0 [388] Biology, Bioinformatics, Neuroscience, Imaging
NMRPipe 7.9 [389] Biology, Biochemistry
Novoalign 2.08.02, 3.00.02 [390] Biology, NGS
NWChem 6.5 [391] Chemistry
Oases 0.2.08 [392] Biology, NGS
Olego 1.1.2, 1.1.5, 1.1.6 [393] Biology, NGS, RNA-Seq
OCaml 4.02.3 [394] Programming Languages, Scripting, Development
Octave 3.6.4 [395] Numerical Computation
Oncotator 1.5.2.0, 1.5.3.0, 1.8.0.0 [396] Biology, Genomics
OpenBabel 2.3.2 [397] Biology, Chemistry
OpenCL 1.1 [398] Programming, Library
OpenCV 2.4.8 [399] Computervision
OpenFOAM 2.1.1 [400] Fluid Dynamics
OpenMM 6.2.0 [401] Quantum Chemistry
OrthoFinder 0.2.5 [402] Biology, Genomics
OrthoMCL 2.0.2, 2.0.3, 2.0.7 [403] Biology, Genomics
p4vasp 0.3.29 [404] Molecular, Electronic Structure
Pacbio 2.2.0, 2.3.0 [405] Biology, Bioinformatics, NGS
Package-GFE 20150701 [406] Biology, Genomics
PALES 122 [407] Physics
PAML 4.7, 4.8a, 4.9a [408] Biology, Phylogenetics
Pandaseq 20140808, 20150627 [409] Biology, Bioinformatics, NGS, Sequencing
PAPI 5.1.0.2 [410] Software, Computing
Parallel 20150122 [411] Programming, Languages
ParaView 4.1.0, 4.2.0, 4.3.0 [412] Data Analysis
PartitionFinder 1.0.1, 1.1.1 [413] Biology, Phylogenetics, Evolution
Parflow v615 [414] Ecology, Modeling
PASA 1.5, 2.0-r20150209 [415] Biology, Genomics
PAUP 4.0b10, 4.1a147 [416] Biology, Phylogenetics
PAUDA 1.0.1 [417] Biology, Bioinformatics, Sequence alignment
PBCore 20151201 [418] Biology, Bioinformatics
PBCommand 20151203 [419] Biology, Library
PBJelly 14.7.14, 15.2.20, 15.8.24 [420] Biology, Bioinformatics
pbsdrmaa 1.0.17 [421] Libraries, Torque
p4est 1.1 [422] Library
pbsmrtpipe 20151202 [423] Biology
PeakSplitter 1.0 [424] Biology, Chip-Seq
PEAR 0.9.2, 0.9.6 [425] Biology, NGS
PDT 3.18 [426] Programming, Profiler
Perl 5.16.0 [427] Programming, Language
PerM 0.4.0 [428] Biology, NGS
PETSc 2.3, 3.3 [429] Math, Numerical solvers
PGDSpider 2.0.9.0 [430] Biology, NGS
Phenix 1.8.1069, 1.10.2155 [431] Crystallography
PHYLDOG 20130418 [432] Biology, Genomics, Phylogenetics
Phyluce 20140427, 20151103 [433] Biology, Phylogenetics
PfamScan 1.3 [434] Biology, Genomics
PHITS 2.52, 2.76. 2.82 [435] Physics
PIPE-CLIP 1.1.0 [436] Biology, NGS
Phonopy 1.9.2 [437] Chemistry
PHYLIP 3.696 [438] Biology, Phylogenetics
PhyloBayes 3.3f, 1.4f MPI [439] Biology, Phylogenetics
PhyloNet 3.5.7 [440] Biology, Phylogenetics
Phylosift 1.1 [441] Biology, Genomics, Phylogenetics, Taxonomy
PhyML 3.0, 20121109 [442] Biology, Phylogenetics
Picard 1.72, 1.80, 2.0.1 [443] Biology, NGS
PICRUSt 1.0.0 [444] Biology, Phylogenetics
Piranha 1.2.1 [445] Biology, Phylogenetics
PLAST 1.0 [446] Biology, Bioinformatics
Plink 1.07, 1.90b3 [447] Biology, GWAS
PLINKSEQ 0.10 [448] Biology, Genomics
PluMiST 1.1 [449] Biology, Phylogenetics, Genomics
PolyPhen 2.2.2.r405b [450] Biology, Genomics
Poretools 0.5.0 [451] Biology, Sequencing
POV-Ray 3.7 [452] 3D, Graphics
Preseq 0.0.4 [453] Biology, NGS
Primer3 2.3.4 [454] Biology, Genomics
PRIMUS 1.8.0 [455] Biology, Phylogenetics
PRINSEQ 0.20.4 [456] Biology, Sequencing
Prodigal 2.6.3 [457] Biology, Genomics
ProfessAtQE 2014 [458] Material Science, Molecular Dynamics
Prokka 1.10, 1.11 [459] Biology, Genomics, Bioinformatics, Assembly
ProBABEL 0.4.2, 0.4.3, 0.4.5 [460] Biology, Genomics, GWAS
Probalign 1.4 [461] Biology, Genomics
Proovread 1.03rcl [462] Biology, Genomics, NGS
Proteinortho 4.26, 5.11 [463] Biology, Genomics
PROVEAN 1.1.5 [464] Biology, Genomics
PyHDF 0.9.0 [465] Library, HDF4
Python 2.7.6, 3.5.0 [466] Biology, Genomics, NGS
Pyrad 3.0.63 [467] Biology, Sequencing Alignment, Assembly
QDD 3.1.2 [468] Programming, scripting, language
QIIME 1.5.0 [469] Biology, Ecology
QT 4.8.3 [470] Computer Science
QUAST 2.3 [471] Biology, NGS
Quake 0.3 [472] Biology, Sequencing
Quantas 1.0.4, 1.0.8 [473] Biology, Bioinformatics, NGS
QualiMap 2.1.1 [474] Biology, Sequence alignment
Quickquartet 1.0.0 [475] Biology, Phylogenetics
R Rmpi/2.15.1, 3.0.2, 3.2.0 [476] Statistics, Programming
R2R 1.0.4 [477] Biology, RNA
R8S 1.71, 1.8 [478] Biology, Evolution
RADICAL 0.2 [479] Biology, Phylogenetics, Genomics
RAxML 8.1.23, 8.2.2, 8.2.3 [480] Biology, Phylogenetics
Ray 2.3.1 [481] Biology, Genomics, NGS
REAGO 1.1 [482] Biology, Assembly
REAPR 1.0.18 [483] Biology, Bioinformatics, Assembly
RepeatExplorer 20150506 [484] Biology, Genomics
RepeatMasker 3.3.0 [485] Biology, Genomics
RepeatModeler 1.0.8 [486] Biology, Bioinformatics
Reptile 1.1 [487] Biology, NGS, error correction
RevBayes 1.0.0 [488] Biology, Phylogenetics
riboPicker 0.4.3 [489] Biology, Sequence
RNAhybrid 2.1.1 [490] Biology, Genomics
rRNASelector 1.0.0 [491] Biology, Sequencing
rnaQUAST 1.2.0 [492] Biology, NGS, Sequencing
ROOT 6.0 [493] Data Analysis
Roary 3.4.1 [494] Biology, Genomics
Rosetta 2014wk4 [495] Biology, Structure, Modelling
RSEG 0.4.8 [496] Biology, NGS
RSEM 1.2.19, 1.2.28, 1.2.29 [497] Biology, NGS, RNA-Seq
RSeQC 2.3.7, 2.6.2 [498] Biology, NGS, RNA-Seq
Ruby 1.9.3-p0 [499] Programming, Scripting, Language
Sailfish 0.6.3 [500] Biology, NGS, RNA-Seq
Sambamba 0.5.0-dev, 0.5.1 [501] Biology, NGS
Samstat 1.08 [502] Biology, NGS, Bioinformatics, Sequencing
Samblaster 0.1.14 [503] Biology, NGS
samtools 1.0, 1.1, 1.2 [504] Biology, NGS
SAS 9.3 [505] Statistics, Graphing
SATe 2.2.7 [506] Biology, Phylogenetics
Scala 2.11.5 [507] Programming, Language
Scalablast 2.4.53 [508] Biology, Genomics
Scalpel 0.1.1 [509] Biology, NGS
Shannon 20160211 [510] Biology, RNA-Seq
SHAPEIT 2.5.5 [511] Biology, SNP
Sharcgs 1.2.11 [512] Biology, NGS, Assembly
Schrodinger 2012, 2013 [513] Simulation, chemistry
SCons 2.3.0 [514] Programming
SCRATCH1D 1.0 [515] Biology, Genomics
Scythe 0.991 [516] Biology, NGS
Segemehl 0.1.9 [517] Biology, NGS, Mapper
SEPP 1.0, 3.0 [518] Biology, Phylogenetics, HMM
SGA 0.10.14 [519] Biology, Assembly
Seq-Gen 1.3.3 [520] Biology, Phylogenetics
SeqPrep 0.5 [521] Biology, NGS
Seqmagick 20150923 [522] Biology, Phylogenetics
SeqMap 1.0.13 [523] Biology, NGS
Seqtk 20140729 [524] Biology, NGS
SEQuel 1.0.1 [525] Biology, NGS
SeqyClean 1.8.10 [526] Biology, NGS, Bioinformatics
ShoRAH 20131204 [527] Biology, NGS, quality filter
SHRiMP 2.2.3 [528] Biology, NGS
SICER 1.1 [529] Biology, ChIP-Seq
Sickle 1.200, 1.33 [530] Biology, NGS, quality filter
Siesta 2.0.2,3.1 [531] Simulation, Physics, Ab Initio
SIFT 4.0.3b [532] Biology, Genomics
SignalP 4.1c [533] Biology, NGS
Silo 4.7 [534] Library, Data
SIPeS 2.0 [535] Biology, Bioinformatics, ChIP-Seq
Slicer 4.3.1 [536] Biology, Imaging
SMALT 0.7.6 [537] Biology, NGS
Snap 20100728 [538] Biology, Genomics
SNAPE-pooled 20130407 [539] Biology, SNP
SNeP 1.1 [540] Biology, Phylogenics
SnpEff 4.0e, 4.1i, 4.2 [541] Biology, NGS, Genomics
SNPhylo 20140701 [542] Bilogy, Phylogenetics
SNP-sites 2.0.3 [543] Biology, SNP
Snippy 20160419 [544] Biology, Phylogenetics
SOAPdenovo 1.05 [545] Biology, NGS
SOAPdenovo-Trans 1.01, 1.03 [546] Biology, NGS
SOAPsplice 1.10 [547] Biology, NGS
SortMeRNA 2.1 [548] Biology, Sequencing, NGS
SparCC 201402 [549] Microbial Ecology
Spades 3.6.2, 3.7.1, 3.8.0 [550] Biology, NGS
Spanki 0.4.1, 0.4.3, 0.5.0 [551] Biology, NGS, RNA-Seq
SPARTA+ 2.60 [552] Chemistry
Spidey 20150922 [553] Biology, Genomics
SPIMAP 1.1 [554] Biology, Phylogenetics
SpliceTrap 0.90.5 [555] Biology, NGS, RNA-Seq
SPM 8 [556] Biology, Statistics, Neurology, Imaging
Sputnik 1.0 [557] Biology, Genomics
SQLite 3.8.8.2 [558] Database
SQL_Developer 4.1.2 [559] Programming, Oracle, Sql
SRA 2.1.10 [560] biology, NGS
SSPACE 2.0, 3.0 [561] Biology, NGS
SSR_pipeline 0.951 [562] Bilogy, DNA Sequencing
Stacks 1.21, 1.24, 1.35 [563] Biology, Genomics, NGS
Staden 1.14.6 [564] Biology, Sequencing
STAR 2.4.0j, 2.5.1b [565] Biology, NGS, Alignment
STAR-CCM+ 8.06 [566] Mechanical Engineering
Stata 10.1, 13 [567] Statistics, Data analysis
Stringtie 1.0.0, 1.1.2, 1.2.1 [568] Biology, NGS, Alignment
Structure 2.3.3, 2.3.4 [569] Biology, Population
Subread 1.5.0-p1 [570] Biology, Sequencing, SNP
SUNDIALS 2.3.0, 2.5.0 [571] Numerical Solver
SVDetect 0.8b [572] Biology, NGS, SNP
swak4Foam 2.x [573] Fluid Dynamics
swarm 1.2.11 [574] Data Analysis
Swig 2.0.9 [575] Programming, C, C++, Python
SwitchSeq 20140907 [576] Biology, NGS
Syzygy 1.2.7 [577] Biology, Genomics
TetGen 1.5.0 [578] Tetrahedral Meshes 3D
TASSEL 5.0 [579] Biology, Genomics
TAU 2.21.4, 2.23 [580] Profiling, Tracing, Programming
T-Coffee 9.03.r1318 [581] Biology, Genomics, Multiple Alignment
TESS 2.3.1 [582] Biology, Genomics, Markov
tgicl 2.1 [583] Biology, sequencing, clustering
Tmux 2.0 [584] GNU, Terminal Multiplexer
TomoPy 0.0.3 [585] Biology, Neuroimaging
Tophat 1.4.1, 2.0.13, 2.1.0 [586] Biology, NGS
Torch 20151107 [587] Lua
Totalview 8.12.0 [588] Computer Science
TPP 4.7.0 [589] Bioinformatics, MassSpec
TrackTools 2011 [590] Bioinformatics
TrackVis 0.5.2.2 [591] Biology, Spectroscopy
Tracula 5.3.2014_05_26 [592] Biology, Bioinformatics, Neuroscience, Imaging
TraitRate 1.1 [593] Biology, Evolution
Trans-ABySS 1.5.4 [594] Biology, Phylogenetics
TransDecoder 20140704, 2.0.1, 3.0.0 [595] Biology, NGS
Transrate 1.0.1 [596] Biology, Assembly
TraCeR 20160519 [597] Biology, Bioinformatics
TreeCorr 3.2.3 [598] Physics
TreeFix 1.1.7, 1.1.10 [599] Biology, Phylogenetics
TreeMix 1.12 [600] Biology, Phylogenetics
TreePL 20150305 [601] Biology, Phylogenetics
TriMetAss 1.1 [602] Biology, Bioinformatics, NGS
TRF 4.04 [603] Biology, Genomics
Trilinos 11.4.1, 11.8.1 [604] Math Algorithm
trimAl 1.2 [605] Biology, Genomics, Sequence Alignment
Trim Galore 0.2.8, 0.4.1 [606] Biology, NGS
Trimmomatic 0.32, 0.33, 0.36 [607] Biology, NGS
Trinity r20151015-2.1.1, r20160329-2.2.0 [608] Biology, NGS, RNA-Seq
Trinotate 2.0.1, 3.0.1 [609] Biology
TRNAscan-SE 1.23 [610] Biology, NGS, Bioinformatics
Twinscan 4.1.2 [611] Biology, Genomics
usearch 7.0.1001-64, 8.0.1517 [612] Biology, Sequence analysis
UDUNITS 2.2.17 [613] Library, Units, Programming
UNAFold 3.8 [614] Biology, Genome, RNA, Folding
UProC 1.2.0 [615] Biology, Genomics
Valgrind 3.9.0 [616] Computer Science
VarScan 2.3.6 [617] Biology, NGS, Genomics
VASP 5.3.2, 5.3.3, 5.3.5, 5.4.1 [618] Quantum Chemistry, Ab Initio
VAST-TOOLS 20150506 [619] Biology, NGS, RNA-Seq
VCFLib 20141119, 20150313 [620] Biology, NGS, Genomics
VCFtools 0.1.12a, 0.1.12b, 0.1.14 [621] Biology, SNPs
velvet 1.2.06, 1.2.07, 1.2.10 [622] Biology, Genomics, NGS
VEP 74, 83 [623] Biology, NGS
VICUNA 1.3 [624] Biology, Assembly
Vim 7.4.5 [625] Programming, Scripting, Language
vmd 1.9.1 [626] Biology, Visualization
VSearch 20151022 [627] Biology, NGS
VT 20140903, 20160129 [628] Biology, Genomics
VTK 6.1.0 [629] Visualization, Graphics
V-Phaser2 02112013 [630] Biology, Phylogenetics
Wannier90 1.2, 2.0.0 [631] Computational Physics
WebLogo 3.3 [632] Biology, Genomics
WDSSII 1 [633] Meteorology
WIEN2k 12.1 [634] Material Science, Chemistry
Wgs or Celera 8.2, 8.3rc1, 8.3rc1.r4638 [635] Biology, NGS
wublast 2.0 [636] Biology, Sequence Alignment
YAHA 0.1.82 [637] Biology NGS
XCrySDen 1.5.60 [638] Computational Material Science
Yambo 3.3.0 [639] Physics
YASM 1.3.0 [640] Computer Science
Yasra 2.32 [641] Biology, NGS
Zagros 1.0.0 [642] Biology, NGS
Zeo++ 0.2.2 [643] Chemistry
Zorro 2.2 [644] Biology, Sequencing
  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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