Difference between revisions of "Installed Software"

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Line 1,147: Line 1,147:
 
| [[SparCC]] || 201402 || [https://bitbucket.org/yonatanf/sparcc/overview] || Microbial Ecology
 
| [[SparCC]] || 201402 || [https://bitbucket.org/yonatanf/sparcc/overview] || Microbial Ecology
 
|-
 
|-
−
| [[Spades]] || 3.6.2, 3.7.1, 3.8.0 || [http://bioinf.spbau.ru/en/spades] || Biology, NGS
+
| [[Spades]] || 3.7.1, 3.8.0, 3.9.0 || [http://bioinf.spbau.ru/en/spades] || Biology, NGS
 
|-
 
|-
 
| [[Spanki]] || 0.4.1, 0.4.3, 0.5.0 || [http://www.cbcb.umd.edu/software/spanki/] || Biology, NGS, RNA-Seq
 
| [[Spanki]] || 0.4.1, 0.4.3, 0.5.0 || [http://www.cbcb.umd.edu/software/spanki/] || Biology, NGS, RNA-Seq

Revision as of 12:53, 28 July 2016

  • Last updated on 2016-07-28.
  • 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 2.0.0, 2.0.2 [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 4.8.0, 4.10.6, 4.10.7 [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
BALI-PHY 2.3.8 [31] Bioinformatics, Bayesian Estimation
BAMM 2.5.0 [32] Biology, Phylogenetics
Bam-readcount 20150216 [33] Biology, NGS
Bamstats 20140602 [34] Biology, NGS
Bamtools 2.1.1 [35] Biology, NGS
BamUtil 1.0.2 [36] Biology, NGS
Bam-Readcount 20150616 [37]] Biology, Genomics
BAPS 6.0 [38] Biology, Populaton genetics
Barrnap 0.7 [39] Biology, RNA-Seq
Basemount 0.1.2.464 [40] Biology, DNA Sequencing
BayArea 1.0.2 [41] Biology
BayesRate 1.3.43 [42] Biology, Phylogenetics
Bbcp 12.08.17.00.0 [43] Network file transfer
Bcbio-nextgen 0.8.7 [44] Biology, NGS
Bcftools 1.0, 1.2, 1.3.1 [45] Biology, Genomics, NGS
Bcl2fastq 2.16 [46] Biology, NGS, Illumina
BEAGLE 3.2.2, 4.0 [47] Biology, Genetics, Genotyping
BEAST 1.7.5, 1.8.1, 2.3.2 [48] Biology, Phylogenetics
Bedops 2.4.2 [49] Biology, Bioinformatics, Sequence, NGS
BEDTools 2.17.0, 2.23.0, 2.24.0 [50] Biology, NGS
BEST 2.3.1 [51] Biology, Phylogenetics
BETA 1.0.5 [52] Biology, NGS
BFAST 0.7.0 [53] Biology, NGS
Bismark 0.7.4, 0.7.7, 0.13.0 [54] Biology, NGS, Methylation
BinPacker 1.0 [55] Biology, RNA-Seq, Sequence Assembly
Bioconductor Latest [56] Biology, R, Statistics
BioPerl 1.006901 [57] Biology, Perl
BioPython 1.59 [58] Biology, Python
BLASR 20130815 [59] Biology, NGS
NCBI BLAST 2.2.27, 2.2.29, 2.4.0 [60] Biology, Sequence alignment
Blast2go 2.5.0-20120705 [61] Biology, Annotation
BLAT 20120524 [62] Biology, Sequence alignment
Blender 2.63 [63] Graphics
BLUPF90 20160604 [64] Biology, Phylogenetics
BoltzTraP 1.2.5 [65] Physics
Boost 1.49.0, 1.53.0, 1.54.0 [66] C++, Library
Bowtie 0.12.9, 1.0.0, 1.1.1 [67] Biology, NGS
Bowtie2 2.2.6, 2.2.8, 2.2.9 [68] Biology, NGS
BPP 1.9.0, 2.2, 3.2 [69] Biology, Phylogenetics
BRANCH 1.8.1 [70] Biology, NGS, Mapping
BRATNextGen 20150505 [71] Biology, Genomics
BRIG 0.95 [72] Biology, Genomics
Bsoft 1.9.1 [73] Biology, Image Analysis
Bsmap 2.74, 2.87 [74] Biology, NGS, Methylation
BUCKy 1.4.4 [75] Biology, Genomics
Busco 1.1b1 [76] Biology, Genomics
Bwa 0.6.1, 0.7.12, 0.7.15 [77] Biology, NGS
BXH_XCEDE_tools 1.11.1 [78] Biology, Bioinformatics
Camino 20140723 [79] Biology, Neuroscience, Imaging
Canu 1.0, 1.1 [80] Biology, Sequencing
CAP3 20120705 [81] Biology, Sequence Assembly
CASAVA 1.8.2 [82] Biology, NGS
CD-HIT 4.6, 4.6.4 [83] Biology, Genomics
CDO 1.6.1, 1.7.2rc5 [84] Climate
CEAS 1.0.2 [85] Biology, Genomics
CellProfiler 2.0 [86] Biology, Image Analysis
CFITSIO 3.370 [87] Library, C
CGATools 1.6.0.42 [88] Biology, NGS
Charmm 36a3 [89] Simulation, Chemistry
Chartdirector 5.1.0 [90] Graphics
CheckM 1.0.4 [91] Biology, Genomics
Chimera 1.7 [92] Biology, Modeling
ChromEvol 2.0 [93] Biology, Phylogenetics
CIMS 4.1.2 [94] Biology, Genomics
Circos 0.63-pre11, 0.69-2 [95] Biology, Visualization
CisGenome 2.0 [96] Biology, Genomics, Peak Calling
Clann 3.2.3 [97] Biology, Phylogenetics
CLARK 1.2.2-b [98] Biology, Genomics
CLHEP 2.2.0.1 [99] High Energy Physics
CLIPper 1.0 [100] Biology, Sequencing
CLIPSeqTools 0.1.7 [101] Biology, Sequencing
ClonalFrame 1.1, 1.2 [102] Biology, Genomics, NGS
ClonalFrameML 1.25 [103] Biology, Genomics, NGS
ClustalW 2.1 [104] Biology, Genomics
Cluster3 1.52 [105] Biology, Genomics
Clview 20130402 [106] Biology, Genomics
ClustalO 1.2.0 [107] Biology, Genomics
ClusterFinder 313 [108] Biology, Metabolomics
CMake 2.8.8, 2.9.12.1, 3.1.0 [109] Programming, Build System
CMWP 140518 [110] Biology, Genomics
CNVnator 0.3.2 [111] Biology, Genomics
CNVSeq 20110715 [112] Biology, NGS
Cobrapy 0.3.2 [113] Biology, Metabolomics, Modeling
Coevol 1.3c, 1.4b [114] Biology, Phylogenetics
CoMap 1.4.1 [115] Biology, Genomics
CONSEL 0.20 [116] Biology, Phylogenetcs
CONCOCT 0.3.1 [117] Biology, Genomics
CoNIFER 0.2.2 [118] Biology, Genomics
Consed 23.0 [119] Biology, Genomics
Coreutils 8.23 [120] GNU Utilities, Computer Science
covNMR 2014 [121] Biochemistry
CPLEX 12.6.5 [122] Optimizer
CUDA 4.2, 5.5 [123] Programming, Graphics
CrossMap 0.2.3 [124] Biology, Genomics
Crux 1.40 [125] Biology, Mass-Spectrometry
Cufflinks 1.3.0, 2.0.2, 2.2.1 [126] Biology, NGS
Cutadapt 1.7.1, 1.8.1, 1.10 [127] Biology, NGS
CUTE 20160116 [128] Cosmology
DAKOTA 5.4.0 [129] Computational Science
DaPars 0.9.0 [130] Biology, NGS, RNA-Seq
DALIGNER 1.0 [131] Biology, Sequencing
Datamash 1.1.0 [132] Math
DCMTK 3.6.0 [133] Biology, Neuroscience, Imaging
DSSAT 4.5 [134] Biology
dDocent 20160425 [135] Biology
DDSCAT 7.3.0 [136] Astrophysics
DDT 4.1.0, 4.2.1 [137] Software
Dealii 8.3.0 [138] Library
DeconSeq 0.4.3 [139] Biology, Phylogenetics
Delft3D 3621 [140] Hydrodynamics, Physics
Desmond 3.0.3.1 [141] Simulation, Biology, Chemistry
DETONATE 1.9, 1.11 [142] Biology, NGS
DEXTRACTOR 1.0 [143] Biology, Sequencing
Dalton 2011 [144] Quantum Chemistry
Diamond 0.5.1, 0.8.5 [145] Computational Biology, Genomics
Dibig Tools 1.0 [146] Bioinformatics, PBS, Torque, Jobs
DiffReps 1.55.4 [147] Biology, NGS, ChIP-Seq
Dindel 1.01 [148] Biology, NGS
DISCOVARdenovo 52488 [149] Biology, NGS
DIYABC 1.0.4.43b, 2.0.3 [150] Biology, Genomics
Dlpoly 4.03.4 [151] Simulation, Biology, Chemistry
Dlpoly-Classic 1.9 [152] Simulation, Biology, Chemistry
DNA Clust 3.0 [153] Biology, Genomics
Dock 6.5, 6.6, 6.7 [154] Chemistry, ligand binding prediction
DOT 2.0 [155] Biology, Bioinformatics, Docking
Doxygen 1.8.3.1 [156] Programming, Documentation
DSSP 2.2.1 [157] Biology, Molecular Dynamics
DTI-TK 2.3.1 [158] Biology, Neurology, Imaging
EA-Utils 1.1.2.537 [159] Biology, NGS
ECTools 20140311, 20141201 [160] Biology, Sequencing, Bioinformatics
EEGLAB 12.0.2.1b, 13.2.2b, 13.4.4b [161] Biology, Matlab
ED2 2.1 [162] Biology
eGene-MVN 0.1 [163] Biology, Genetics
eigenMT 20160228 [164] Biology, Genetics
EIGENSOFT 4.2, 5.0.1, 6.0.1 [165] Biology, Population
emboss 6.5.7 [166] Biology, multi-tool suite
EMAN2 2.11 [167] Biology
EMIRGE 20130727 [168] Biology, NGS
Ensembl_Tools 80 [169] Biology, Bioinformatics
EPACTS 3.2.6 [170] Biology, Bioinformatics, Genomics
EPOCH 4.7.3 [171] Astronomy, CPPP
eQTLA 1.1 [172] Biology, Genomics
Eqtlbma 1.2.2 [173] Biology, Genotyping
Esmf 6.3.0rp1 [174] Climate
Espresso 5.0.1, 5.2.0, 5.2.1, 5.3.0 [175] Modeling, Physics
ESPRIT 201211 [176] Biology, NGS, Metagenomics
ETE2 2.1 [177] Biology, Phylogenetics
Eval 2.2.8 [178] Biology, Genomics, GUI
ExaBayes 1.2.1, 1.4.1 [179] Biology, Phylogenetics
ExaML 1.0.5, 1.0.12, 3.0.14, 3.0.17 [180] Biology, Phylogenetics
ExomeCNV 1.4 [181] Biology, NGS, Genomics
Exonerate 2.2.0 [182] Biology, Genomics
eXpress 1.3.1 [183] Biology, NGS
FALCON 20130305, 20160108 [184] Biology, Bioinformatics, NGS, Sequencing
FALCON_unzip 20160623 [185] Biology, Bioinformatics
FAR 2.15 [186] Biology, Genomics
FASTA 34.26.5, 36.3.6d [187] Biology, Genomics
FAST-iCLIP 0.9.1 [188] Biology, Sequencing
FastML 3.0 [189] Biology, Phylogenetics, ML
FastQC 0.10.1, 0.11.2, 0.11.4 [190] Biology, NGS
Fastq-tools 0.7, 0.8 [191] Biology, NGS
FastStructure 20150112 [192] Biology, Genomics
FastTree 2.1.7 [193] Biology, Phylogenetics
Fastx_toolkit 0.0.13.2 [194] Biology, NGS
Fathmm 20150225 [195] Biology, Genomics
fcGENE 1.0.7 [196] Biology, Genomics, SNP
Ferret 6.82 [197] Oceanography, Meteorology
FFmpeg 2.1.3, 2.8.3 [198] Multimedia, audio, video
FFTW 3.3.2, 3.3.3, 3.3.4 [199] Math, Library, C++
FineSTRUCTURE 2.0.7 [200] Biology, Populatiopn Genetics
FLASH 1.2.10, 1.2.11 [201] Biology, Genomics, NGS
Flexbar 2.3 [202] Biology, Genomics, NGS
Fluent 14.5.7, 15.0.7, 16.0 [203] Simulation, Fluid Dynamics
FragGeneScan 1.16 [204] Biology, NGS, Genomics
FrameDP 1.2.2 [205] Biology, Sequencing
FreeBayes 0.9.21, 1.0.1, 1.0.2 [206] Biology, NGS, SNP Calling
Freesurfer 5.2.0, 5.3.0 [207] Biology, Neurology, Imaging
FSL 5.0.2.2 [208] Biology, Neurology, Imaging
Galaxy latest [209] Biology, Chemistry, Other
GapFiller 1.11 [210] Biology, NGS
Garli 2.0, 2.01 [211] Biology, Phylogenetics
GAML 20150610 [212] Biology, NGS
GAMBIT 15.1.0 [213] Game Theory
GARM 0.7.4 [214] Biology, NGS
GASVPro 201310 [215] Biology, NGS, Genomics
GATE 7.0 [216] Data Analysis
GATK 1.6.9, 3.4.46, 3.5.0 [217] Biology, NGS
Gaussian G03, G09-A.02, G09-C.01 [218] Modeling, Computational Chemistry
Gblocks 0.91b [219] Genomics, Alignment tool
GCTA 1.24.7 [220] Biology, Genomics, SNP
GDAL 1.11.2 [221] Geospatial Data Modeling, Geospatial Library
GDC-Client 1.0.1 [222] Biology, Bioinformatics, Sequencing, NGS
Geant4 4.10 [223] Physics
GEM 20130406 [224] Biology, NGS
GEMINI 4.6.6a, 0.13.1, 0.18.0 [225] Biology, Genomics, Genetics
GenBank Tools 20140130 [226] Biology, Genomics
GeneMark 2012.04 [227] Biology, Genomics, Metagenomics
GeneSeqer 20140226 [228] Biology, Genomics
Genewise 2.2.0 [229] Biology, Genomics, Annotation
Genome STRiP 2.00.1602 [230] Biology, genomics, NGS
GenomicConsensus 20160523 [231] Biology, Phylogenetics
GenomicTools 2.7.0 [232] Biology, NGS
GenomeTools 1.5.7 [233] Biology, Bioinformatics
GenSel 4.90 [234] Biology, Genetics
GET_HOMOLOGUES 20150529 [235] Biology, Genomics
GKNO 1.30.18 [236] Biology, NGS,
Git 1.8.2.1, 1.9.0 [237] Development, Revision Control
Glimmer 3.02 [238] Biology, Microbial Annotation
Globus 2.1.3 [239] Data Transfer
GLPK 4.55 [240] Biology, Genomics
Gmap 20150612, 20150723, 20160501 [241] Biology, Genomics
GNU Compilers 5.2.0 [242] Compilers, Programming
GnuPlot 4.6.0, 5.0.3 [243] Graphics, Plotting, Programming
Grace 5.1.22 [244] Graphics, plotting, 2D
GrADS 2.0.1 [245] Earth Science
GramCluster 1.3 [246] Biology, Sequencing
GraphViz 2.38.0 [247] Graphics, plotting, visualization
Gromacs 4.5.5, 4.6.5, 5.1.2 [248] Chemistry, Modeling, Simulation
GSNP 1.0 [249] Biology, Bioinformatics, NGS
GSL 1.15 [250] Library, Math, C++, C
Gsutil 4.15 [251] Cloud, Storage, Google
Gubbins 20150519, 20160421 [252] Biology, Phylogenetics, Genomics
GULP 4.0 [253] Material Science
HaMStR 13.2.2, 13.2.3, 13.2.4 [254] Biology, Genomics
HapCompass 0.7.7 [255] Biology, NGS, Genomics
HAPCUT 0.7 [256] Biology, Assembly
Hapsembler 2.21 [257] Biology, Genomics, NGS
HapTree 1.0 [258] Biology, Genomics, NGS
HDF4 4.2.11 [259] Library, Data
HDF5 1.8.9, 1.8.12, 1.8.15 [260] Library, Data
HISAT2 2.0.0b, 2.0.1b, 2.0.3b [261] Biology, Sequence Alignment, NGS
HMMER3 3.0, 3.1b1, 3.1b2 [262] Biology, Genomics
HMMSplicer 0.9.5 [263] Biology, Genomics
HOMER 4.2, 4.7, 4.8 [264] Biology, Genomics
HOOMD 1.3.3 [265] Chemistry
HTMLDoc 1.2.82 [266] Documentation, PDF, HTML
HTSeq 0.5.3p3, 0.6.1p1 [267] Biology, NGS
Hyb 20141126 [268] Biology, NGS, RNA-Seq
HyPhy 2.1.2.28, 2.2.6.1 [269] Biology, Phylogenetics
Hypre 1.10.0b, 2.8.0b [270] Library, Math, Physics
iAssembler 1.32 [271] Biology, Assembly
IBDNe 20150815 [272] Biology, NGS
ICORN2 0.95 [273] Biology, Sequencing
IDBA-UD 1.0.9, 1.1.0, 1.1.1 [274] Biology, NGS
IDBA-MT 1.0 [275] Biology, NGS
IEP 3.6 [276] Programming, Python, Editor
IGB 8.4.1 [277] Biology, Genomics, NGS
iGTP 1.1 [278] Biology, Bioinformatics, Phylogenetics
illumiprocessor 20150803 [279] Biology, Sequencing
IM and IMa 20091217 [280] Biology, Population
IMa2 20120827 [281] Biology, Population
ImageJ 1.48 [282] Image manipulation
ImageMagick 6.8.8-9 [283] Image manipulation
Intel Compilers 2016.0.109 [284] Programming, Compilers
IOAPI 3.1 [285] Meteorology
Iprscan 4.8 [286] Biology, Genomics
IQ-TREE 1.3.11, 1.4.0, 1.4.2 [287] Biology, Phylogenetics
ITK 4.3.1 [288] Biology, Genomics
ITK-SNAP 3.0.0 [289] Biology, Neuroscience, Imaging
JAGS 3.3.0 [290] Statistics
Java 1.7.0_79, 1.8.0_31 [291] Java Development Kit
Je 1.0. [292] Biology, NGS
Jellyfish 2.1.1 [293] Biology, NGS
JModelTest 2.1.1 [294] Biology, Phylogenetics, Genomics
Julia 0.3.11, 0.4.6 [295] Programming, Languages
KaKs 1.2 [296] Biology, Phylogenetics
Kent 20120524 [297] Biology, NGS
Khmer 1.1, 2.0 [298] Biology, NGS
KING 1.4, 1.9 [299] Biology, Genomics
Kallisto 0.42.3, 0.42.4 [300] Biology, NGS, RNA-Seq
Kmer 1934 [301] Biology, NGS
KmerGenie 1.6741 [302] Biology, NGS, Utilities
Kraken 0.10.4b [303] Biology, Genomics, Phylogenetics
LAMMPS 28Oct12, 30Sep13, 28Jun14,15May15, 7Dec15 [304] Molecular Dynamics Simulation
LAMP 2.5 [305] Biology, Genomics
Last 193, 247 [306] Biology, Sequence alignment
Lastz 1.03.02, 1.02.00 [307] Biology, NGS
LDhat 2.2a [308] Biology, Genomics
LIBSVM 3.12 [309] Machine Learning
LIGR 2.05 [310] Biology, Assembly
LFMM 1.4 [311] Biology, Genomics
LSC 0.3, 0.3.1 [312] Biology, NGS, Error correction
Loci 3.3 [313] Fluid Dynamics
LS-DYNA 700, 711, 800 [314] Physics
Lumpy 0.2.1 [315] Biology, SNP
LZO 2.09 [316] Library, Data Compression
MACH 1.0.18 [317] Biology, Genomics
Mach2VCF 20150515 [318] Biology
M5tools 20121126 [319] Biology, Bioinformatics, Genomics
MACS 1.4.2 [320] Biology, ChIP-Seq
mafft 7.215, 7.245, 7.294 [321] Biology, Multiple sequence alignment
Mash 1.1 [322] Biology, Genomics
Maker 2.25b, 2.31.6, 2.31.8 [323] Biology, Annotation, Genomics
MapSplice 2.1.7 [324] Biology, NGS, RNA-Seq
MAPminer 1.1 [325] Biology, Phylogenetics
MassMine 0.9.5, 0.10.0, 0.11.0 [326] Data Mining
Maq 0.7.1 [327] Biology, NGS
MARK 2.0.1 [328] Statistics
MarkerMiner 20150429, 20150511 [329] Biology, Genomics
MaSuRCA 2.3.2 [330] Biology, NGS
Matlab 2012a, 2013a, 2014a [331] Math, Simulation, Programming
MATS 2.1.0, 3.0.8, 3.0.9 [332] BIology, NGS
Mauve 2.3.1 [333] Biology, NGS
MaxBin 2.1.1 [334] Biology, NGS
MCarts 1.0.2 [335] Biology, Genomics, Markov models
MCNP 5, 6b2, 6 [336] Physics
MCNPX 2.7.0, 2.7.0-i8 [337] Physics
MEGAN 5.10.3, 6.4.15 [338] Biology, NGS
Megraft 1.0.2 [339] Biology, Sequencing
Melting 4.3.1 [340] Biology, Genome, RNA, Folding
Meme 4.8.1 [341] Biology, Motifs, Sequence analysis
Meraculous 2.0.5 [342] Biology, NGS
Mercurial 2.7 [343] Development, Revision Control
Merlin 1.1.2 [344] Biogolgy, SNP
Meta-Tissue 0.4 [345] Biology, Genetics
Metabin 1.0 [346] Biology, Metagenomics
MetaCluster 5.0b [347] Biology, Metagenomics
MetaCV 2.3.0 [348] Biology, NGS
METAL 20110325 [349] Biology, Genomics
MetAMOS 1.5.0rc4-20140827 [350] Biology, Bioinformatics, Genomics, Assembly
Metassembler 1.5 [351] Biology, Genomics
MetaVelvet 1.2.01 [352] Biology, NGS
Metaxa2 2.0.2, 2.1.1 [353] Biology, NGS
MetaGeneMark 2012.04 [354] Biology, Genomics
Mfold 3.6 [355] Biology, Genomics
MGEScan 1.1 [356] Biology, Genomics
MHAP 1.6 [357] Biology, Sequencing
MIA 20130301 [358] Biology, NGS
Midnight Commander 4.6.1 [359] Tools, Utilities
Migrate-n 3.3.0, 3.6.6 [360] Biology, Population
Minced 0.2.0 [361] Biology, Genomics
Minimac 2-20140915, 3-20151015 [362] Biology, Genomics
mira 3.9.18, 4.0.rc1, 4.0.2 [363] Biology, NGS
MISO 0.4.9, 0.5.2, 0.5.3 [364] Biology, NGS
MMSEQ 1.0.8 [365] Biology, NGS
MSMBuilder 2.5.1 [366] Molecular Dynamics
MOABS 1.2.9, 1.3.2, 1.3.4 [367] Biology, NGS, Genomics
Modeller 9.11, 9.13, 9.14 [368] Biology, Modeling
Molden 5.0 [369] Molecular, electronic structure
MolPro 2012.1p22 [370] Quantum Chemistry, Ab Initio
mosaik 2.1.33, 2.2.3 [371] Biology,NGS
Mothur 1.31.2, 1.36.1, 1.37.0 [372] Biology, Microbial Ecology
MOTU 1.1 [373] Biology, Bioinformatics, Genomics
MPE2 2.4.9b [374] MPI
MP-EST 1.4, 1.5 [375] Biology, Phylogenetics
mpiP 3.4.1 [376] Parallel Computing
MrBayes 3.2.1, 3.2.4, 3.2.5 [377] Biology, Phylogenetics
MRIcron 201306 [378] Biology, MRI, Imaging
MUMmer 3.23 [379] Biology, Genomics
MUSCLE 3.8.31 [380] Biology, Genomics
MuTect 1.1.4, 1.1.7 [381] Biology, Genomics
MutSig 1.4 [382] Biology, Genomics
MZMine 2.15, 2.17, 2.19 [383] Biology, Spectroscopy
NAMD 2.9 [384] Simulation, Chemistry, Biology
Nanocorrect 20150727 [385] Biology, NGS
Nanopolish 20150904 [386] Biology
Nbody 6 [387] Astronomy
NCBI C++ Toolkit 12.0.0 [388] Biology, C++, Development
NCL 6.1.2, 6.3.0 [389] Atmosphere Science
NCO 4.2.1, 4.4.3 [390] Data exchange tools
Ncview 2.1.2 [391] Data visualization
NetCDF 3.4.2, 4.2, 4.3 [392] Data exchange, Tools
Newbler 2.7, 2.8, 2.9 [393] Biology, NGS
Newick utils 1.6 [394] Biology, Phylogenetics
Nextallele 20140718 [395] Biology, Genomics
Nexus NCL 2.1.18 [396] Biology, Phylogenetics, Library
ngsCAT 0.1 [397] Biology, Bioinformatics, NGS
ngsTools 20150816 [398] Biology, NGS
NGSUtils 20130722, 20150206 [399] Biology, NGS
Nipype 0.10.0 [400] Biology, Bioinformatics, Neuroscience, Imaging
NMRPipe 7.9 [401] Biology, Biochemistry
Novoalign 2.08.02, 3.00.02 [402] Biology, NGS
NWChem 6.5, 6.6 [403] Chemistry
Oases 0.2.08 [404] Biology, NGS
Olego 1.1.2, 1.1.5, 1.1.6 [405] Biology, NGS, RNA-Seq
OCaml 4.02.3 [406] Programming Languages, Scripting, Development
Octave 3.6.4 [407] Numerical Computation
Oncotator 1.5.2.0, 1.5.3.0, 1.8.0.0 [408] Biology, Genomics
OpenBabel 2.3.2 [409] Biology, Chemistry
OpenCL 1.1 [410] Programming, Library
OpenCV 2.4.8 [411] Computervision
OpenFOAM 2.1.1 [412] Fluid Dynamics
OpenMM 6.2.0 [413] Quantum Chemistry
OrthoFinder 0.2.5 [414] Biology, Genomics
OrthoMCL 2.0.2, 2.0.3, 2.0.7 [415] Biology, Genomics
p4vasp 0.3.29 [416] Molecular, Electronic Structure
Pacbio 2.2.0, 2.3.0 [417] Biology, Bioinformatics, NGS
Package-GFE 20150701 [418] Biology, Genomics
PALES 122 [419] Physics
PAML 4.7, 4.8a, 4.9a [420] Biology, Phylogenetics
Pandaseq 20140808, 20150627 [421] Biology, Bioinformatics, NGS, Sequencing
PAPI 5.1.0.2 [422] Software, Computing
Parallel 20150122 [423] Programming, Languages
ParaView 4.1.0, 4.2.0, 4.3.0 [424] Data Analysis
Parsimonator 1.0.2 [425] Biology, Bioinformatics
PartitionFinder 1.0.1, 1.1.1 [426] Biology, Phylogenetics, Evolution
Parflow v615 [427] Ecology, Modeling
PASA 1.5, 2.0-r20150209 [428] Biology, Genomics
PASTA 20160616 [429] Biology, Sequence alignment,
PAUP 4.0b10, 4.1a147 [430] Biology, Phylogenetics
PAUDA 1.0.1 [431] Biology, Bioinformatics, Sequence alignment
PBCore 20151201 [432] Biology, Bioinformatics
PBCommand 20151203 [433] Biology, Library
PBJelly 14.7.14, 15.2.20, 15.8.24 [434] Biology, Bioinformatics
pbsdrmaa 1.0.17 [435] Libraries, Torque
p4est 1.1 [436] Library
pbsmrtpipe 20151202 [437] Biology
PeakSplitter 1.0 [438] Biology, Chip-Seq
PEAR 0.9.2, 0.9.6 [439] Biology, NGS
PDT 3.18 [440] Programming, Profiler
Perl 5.16.0 [441] Programming, Language
PerM 0.4.0 [442] Biology, NGS
PETSc 2.3, 3.3 [443] Math, Numerical solvers
PGDSpider 2.0.9.0 [444] Biology, NGS
Phenix 1.8.1069, 1.10.2155 [445] Crystallography
PHYLDOG 20130418 [446] Biology, Genomics, Phylogenetics
Phyluce 20140427, 20151103 [447] Biology, Phylogenetics
PfamScan 1.3 [448] Biology, Genomics
PHITS 2.52, 2.76. 2.82 [449] Physics
PIPE-CLIP 1.1.0 [450] Biology, NGS
Phonopy 1.9.2 [451] Chemistry
PHYLIP 3.696 [452] Biology, Phylogenetics
PhyloBayes 3.3f, 1.4f MPI [453] Biology, Phylogenetics
PhyloNet 3.5.7 [454] Biology, Phylogenetics
Phylosift 1.1 [455] Biology, Genomics, Phylogenetics, Taxonomy
PhyML 3.0, 3.1 [456] Biology, Phylogenetics
Picard 1.72, 1.80, 2.0.1 [457] Biology, NGS
PICRUSt 1.0.0 [458] Biology, Phylogenetics
Piranha 1.2.1 [459] Biology, Phylogenetics
PLAST 1.0 [460] Biology, Bioinformatics
Plink 1.07, 1.90b3 [461] Biology, GWAS
PLINKSEQ 0.10 [462] Biology, Genomics
PluMiST 1.1 [463] Biology, Phylogenetics, Genomics
PolyPhen 2.2.2.r405b [464] Biology, Genomics
Poretools 0.5.0 [465] Biology, Sequencing
POV-Ray 3.7 [466] 3D, Graphics
Preseq 0.0.4 [467] Biology, NGS
Primer3 2.3.4 [468] Biology, Genomics
PRIMUS 1.8.0 [469] Biology, Phylogenetics
PRINSEQ 0.20.4 [470] Biology, Sequencing
Prodigal 2.6.3 [471] Biology, Genomics
ProfessAtQE 2014 [472] Material Science, Molecular Dynamics
Prokka 1.10, 1.11 [473] Biology, Genomics, Bioinformatics, Assembly
ProBABEL 0.4.2, 0.4.3, 0.4.5 [474] Biology, Genomics, GWAS
Probalign 1.4 [475] Biology, Genomics
Proovread 1.03rcl [476] Biology, Genomics, NGS
Proteinortho 4.26, 5.11 [477] Biology, Genomics
PROVEAN 1.1.5 [478] Biology, Genomics
PyHDF 0.9.0 [479] Library, HDF4
Python 2.7.6, 3.5.0 [480] Biology, Genomics, NGS
Pyfasta 0.5.2 [481] Biology, Phylogenetics
Pyrad 3.0.63 [482] Biology, Sequencing Alignment, Assembly
QDD 3.1.2 [483] Programming, scripting, language
QIIME 1.5.0 [484] Biology, Ecology
QT 4.8.3 [485] Computer Science
QUAST 2.3 [486] Biology, NGS
Quake 0.3 [487] Biology, Sequencing
Quantas 1.0.4, 1.0.8 [488] Biology, Bioinformatics, NGS
QualiMap 2.1.1 [489] Biology, Sequence alignment
Quickquartet 1.0.0 [490] Biology, Phylogenetics
R Rmpi/2.15.1, 3.0.2, 3.2.0 [491] Statistics, Programming
R2R 1.0.4 [492] Biology, RNA
R8S 1.71, 1.8 [493] Biology, Evolution
RADICAL 0.2 [494] Biology, Phylogenetics, Genomics
RAxML 8.1.23, 8.2.2, 8.2.3 [495] Biology, Phylogenetics
Ray 2.3.1 [496] Biology, Genomics, NGS
REAGO 1.1 [497] Biology, Assembly
REAPR 1.0.18 [498] Biology, Bioinformatics, Assembly
RELION 1.4 [499] Biology, Bioinformatics
RepeatExplorer 20150506 [500] Biology, Genomics
RepeatMasker 3.3.0 [501] Biology, Genomics
RepeatModeler 1.0.8 [502] Biology, Bioinformatics
Reptile 1.1 [503] Biology, NGS, error correction
RevBayes 1.0.0 [504] Biology, Phylogenetics
riboPicker 0.4.3 [505] Biology, Sequence
RNAhybrid 2.1.1 [506] Biology, Genomics
rRNASelector 1.0.0 [507] Biology, Sequencing
rnaQUAST 1.2.0 [508] Biology, NGS, Sequencing
ROOT 6.0 [509] Data Analysis
Roary 3.4.1 [510] Biology, Genomics
Rosetta 2014wk4 [511] Biology, Structure, Modelling
RSEG 0.4.8 [512] Biology, NGS
RSEM 1.2.19, 1.2.28, 1.2.29 [513] Biology, NGS, RNA-Seq
RSeQC 2.3.7, 2.6.2 [514] Biology, NGS, RNA-Seq
Ruby 1.9.3-p0 [515] Programming, Scripting, Language
Sailfish 0.6.3 [516] Biology, NGS, RNA-Seq
Salmon 0.6.0 [517] Biology, RNA-seq
Sambamba 0.5.0-dev, 0.5.1 [518] Biology, NGS
Samstat 1.08 [519] Biology, NGS, Bioinformatics, Sequencing
Samblaster 0.1.14 [520] Biology, NGS
samtools 1.1, 1.2, 1.3.1 [521] Biology, NGS
SAS 9.3 [522] Statistics, Graphing
SATe 2.2.7 [523] Biology, Phylogenetics
Scala 2.11.5 [524] Programming, Language
Scalablast 2.4.53 [525] Biology, Genomics
Scalpel 0.1.1 [526] Biology, NGS
Shannon 20160211 [527] Biology, RNA-Seq
SHAPEIT 2.5.5 [528] Biology, SNP
Sharcgs 1.2.11 [529] Biology, NGS, Assembly
shustring 2.6 [530] Biology, Sequencing
Schrodinger 2012, 2013 [531] Simulation, chemistry
SCons 2.3.0 [532] Programming
SCRATCH1D 1.0 [533] Biology, Genomics
Scythe 0.991 [534] Biology, NGS
Segemehl 0.1.9 [535] Biology, NGS, Mapper
SEPP 1.0, 3.0 [536] Biology, Phylogenetics, HMM
SGA 0.10.14 [537] Biology, Assembly
Seq-Gen 1.3.3 [538] Biology, Phylogenetics
SeqPrep 0.5 [539] Biology, NGS
Seqmagick 20150923 [540] Biology, Phylogenetics
SeqMap 1.0.13 [541] Biology, NGS
Seqtk 20140729 [542] Biology, NGS
SEQuel 1.0.1 [543] Biology, NGS
SeqyClean 1.8.10 [544] Biology, NGS, Bioinformatics
ShoRAH 20131204 [545] Biology, NGS, quality filter
SHRiMP 2.2.3 [546] Biology, NGS
SICER 1.1 [547] Biology, ChIP-Seq
Sickle 1.200, 1.33 [548] Biology, NGS, quality filter
Siesta 2.0.2,3.1 [549] Simulation, Physics, Ab Initio
SIFT 4.0.3b [550] Biology, Genomics
SignalP 4.1c [551] Biology, NGS
Silo 4.7 [552] Library, Data
SIPeS 2.0 [553] Biology, Bioinformatics, ChIP-Seq
Slicer 4.3.1 [554] Biology, Imaging
SMALT 0.7.6 [555] Biology, NGS
Snap 20100728 [556] Biology, Genomics
SNAPE-pooled 20130407 [557] Biology, SNP
SNeP 1.1 [558] Biology, Phylogenics
SnpEff 4.1i, 4.2, 4.3 [559] Biology, NGS, Genomics
SNPhylo 20140701 [560] Bilogy, Phylogenetics
SNP-sites 2.0.3 [561] Biology, SNP
Snippy 20160419 [562] Biology, Phylogenetics
SOAPdenovo 1.05 [563] Biology, NGS
SOAPdenovo-Trans 1.01, 1.03 [564] Biology, NGS
SOAPsplice 1.10 [565] Biology, NGS
SortMeRNA 2.1 [566] Biology, Sequencing, NGS
SparCC 201402 [567] Microbial Ecology
Spades 3.7.1, 3.8.0, 3.9.0 [568] Biology, NGS
Spanki 0.4.1, 0.4.3, 0.5.0 [569] Biology, NGS, RNA-Seq
SPARTA+ 2.60 [570] Chemistry
Spidey 20150922 [571] Biology, Genomics
SPIMAP 1.1 [572] Biology, Phylogenetics
SpliceTrap 0.90.5 [573] Biology, NGS, RNA-Seq
SPM 8 [574] Biology, Statistics, Neurology, Imaging
Sputnik 1.0 [575] Biology, Genomics
SQLite 3.8.8.2 [576] Database
SQL_Developer 4.1.2 [577] Programming, Oracle, Sql
SRA 2.1.10 [578] biology, NGS
SSPACE 2.0, 3.0 [579] Biology, NGS
SST-Core 6.0.0 [580] MPI
SSR_pipeline 0.951 [581] Bilogy, DNA Sequencing
Stacks 1.21, 1.24, 1.35 [582] Biology, Genomics, NGS
Staden 1.14.6 [583] Biology, Sequencing
STAR 2.4.0j, 2.5.1b [584] Biology, NGS, Alignment
STAR-CCM+ 8.06 [585] Mechanical Engineering
Stata 10.1, 13 [586] Statistics, Data analysis
Stringtie 1.0.0, 1.1.2, 1.2.1 [587] Biology, NGS, Alignment
Structure 2.3.3, 2.3.4 [588] Biology, Population
Subread 1.5.0-p1 [589] Biology, Sequencing, SNP
SUNDIALS 2.3.0, 2.5.0 [590] Numerical Solver
SVDetect 0.8b [591] Biology, NGS, SNP
swak4Foam 2.x [592] Fluid Dynamics
swarm 1.2.11 [593] Data Analysis
Swig 2.0.9 [594] Programming, C, C++, Python
SwitchSeq 20140907 [595] Biology, NGS
Syzygy 1.2.7 [596] Biology, Genomics
TetGen 1.5.0 [597] Tetrahedral Meshes 3D
TASSEL 5.0 [598] Biology, Genomics
TAU 2.21.4, 2.23 [599] Profiling, Tracing, Programming
T-Coffee 9.03.r1318 [600] Biology, Genomics, Multiple Alignment
TESS 2.3.1 [601] Biology, Genomics, Markov
tgicl 2.1 [602] Biology, sequencing, clustering
Tmux 2.0 [603] GNU, Terminal Multiplexer
TomoPy 0.0.3 [604] Biology, Neuroimaging
Tophat 1.4.1, 2.0.13, 2.1.0 [605] Biology, NGS
Torch 20160704 [606] Lua
Totalview 8.12.0 [607] Computer Science
TPP 4.7.0 [608] Bioinformatics, MassSpec
TrackTools 2011 [609] Bioinformatics
TrackVis 0.5.2.2 [610] Biology, Spectroscopy
Tracula 5.3.2014_05_26 [611] Biology, Bioinformatics, Neuroscience, Imaging
TraitRate 1.1 [612] Biology, Evolution
Trans-ABySS 1.5.4 [613] Biology, Phylogenetics
TransDecoder 20140704, 2.0.1, 3.0.0 [614] Biology, NGS
Transrate 1.0.1 [615] Biology, Assembly
TraCeR 20160519 [616] Biology, Bioinformatics
TreeCorr 3.2.3 [617] Physics
TreeFix 1.1.7, 1.1.10 [618] Biology, Phylogenetics
TreeMix 1.12 [619] Biology, Phylogenetics
TreePL 20150305 [620] Biology, Phylogenetics
TriMetAss 1.1 [621] Biology, Bioinformatics, NGS
TRF 4.04 [622] Biology, Genomics
Trilinos 11.4.1, 11.8.1 [623] Math Algorithm
trimAl 1.2 [624] Biology, Genomics, Sequence Alignment
Trim Galore 0.2.8, 0.4.1 [625] Biology, NGS
Trimmomatic 0.32, 0.33, 0.36 [626] Biology, NGS
Trinity r20151015-2.1.1, r20160329-2.2.0 [627] Biology, NGS, RNA-Seq
Trinotate 2.0.1, 3.0.1 [628] Biology
TRNAscan-SE 1.23 [629] Biology, NGS, Bioinformatics
Twinscan 4.1.2 [630] Biology, Genomics
usearch 7.0.1001-64, 8.0.1517 [631] Biology, Sequence analysis
UDUNITS 2.2.17 [632] Library, Units, Programming
UNAFold 3.8 [633] Biology, Genome, RNA, Folding
UProC 1.2.0 [634] Biology, Genomics
Valgrind 3.9.0 [635] Computer Science
VarDictJava 20160521 [636] Biology, NGS
VarScan 2.3.6 [637] Biology, NGS, Genomics
VASP 5.3.2, 5.3.3, 5.3.5, 5.4.1 [638] Quantum Chemistry, Ab Initio
VAST-TOOLS 20150506 [639] Biology, NGS, RNA-Seq
VCFLib 20141119, 20150313 [640] Biology, NGS, Genomics
VCFtools 0.1.12a, 0.1.12b, 0.1.14 [641] Biology, SNPs
velvet 1.2.06, 1.2.07, 1.2.10 [642] Biology, Genomics, NGS
VEP 74, 83 [643] Biology, NGS
VICUNA 1.3 [644] Biology, Assembly
ViennaRNA 2.2.6 [645] Biology, RNA-seq
Vim 7.4.5 [646] Programming, Scripting, Language
vmd 1.9.1 [647] Biology, Visualization
VSearch 20151022 [648] Biology, NGS
VT 20140903, 20160129 [649] Biology, Genomics
VTK 6.1.0 [650] Visualization, Graphics
V-Phaser2 02112013 [651] Biology, Phylogenetics
Wannier90 1.2, 2.0.0 [652] Computational Physics
WebLogo 3.3 [653] Biology, Genomics
WDSSII 1 [654] Meteorology
WIEN2k 12.1 [655] Material Science, Chemistry
Wgs or Celera 8.2, 8.3rc1, 8.3rc1.r4638 [656] Biology, NGS
wublast 2.0 [657] Biology, Sequence Alignment
YAHA 0.1.82 [658] Biology NGS
XCrySDen 1.5.60 [659] Computational Material Science
Yambo 3.3.0 [660] Physics
YASM 1.3.0 [661] Computer Science
Yasra 2.32 [662] Biology, NGS
Zagros 1.0.0 [663] Biology, NGS
Zeo++ 0.2.2 [664] Chemistry
Zorro 2.2 [665] 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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