Difference between revisions of "Installed Software"

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Line 791: Line 791:
 
| [[PHYLDOG]] || 20130418 || [http://pbil.univ-lyon1.fr/software/phyldog] || Biology, Genomics, Phylogenetics
 
| [[PHYLDOG]] || 20130418 || [http://pbil.univ-lyon1.fr/software/phyldog] || Biology, Genomics, Phylogenetics
 
|-
 
|-
−
| [[Phyluce]] || c561dd9 || [https://github.com/faircloth-lab/phyluce] || Biology, Phylogenetics
+
| [[Phyluce]] || 20140427, 20151103 || [https://github.com/faircloth-lab/phyluce] || Biology, Phylogenetics
 
|-
 
|-
 
| [[PfamScan]] || 1.3 || [http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/] || Biology, Genomics
 
| [[PfamScan]] || 1.3 || [http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/] || Biology, Genomics

Revision as of 22:31, 7 December 2015

  • Last updated on 2015-12-07.
  • Up to three latest versions are listed. The default is shown in bold if it's not the latest version.
  • See output of 'module spider module_name' for a full list of provided versions.

A B C D E F G H I J K L M N O P Q R S T U V W X Y

Name Version [1] Website Category
4P 1.0 [1] Biology, SNP
AbInit 6.12.3, 7.10.2, 7.10.4 [2] Quantum Chemistry, DFT
Abyss 1.3.4, 1.3.7, 1.5.2 [3] Biology, NGS
AdmixTools 20150311 [4] Biology, Bioinformatics, Genomics, NGS
ADMIXTURE 1.23 [5] Biology, Bioinformatics, Genomics, NGS
AEGeAn 0.14.0 [6] Biology, Genomics
AFNI 2013_05_31, 2013_11_24 [7] Biology, Statistics, Imaging, Neurology
Agalma 0.2.1, 0.3.5, 0.5.0 [8] Biology, Bioinformatics, Genomics, SNP
ALE 20150507 [9] Biology, Bioinformatics, Assembly
ALLPATHS-LG 42316, 44837 [10] Biology, NGS
Amber 11, 12, 14 [11] Simulation, chemistry
AMOS 3.1.0 [12] Biology, Genomics, NGS
ANNOVAR 20120621, 20150322 [13] Biology, Genomics
AStalavista 3.2 [14] Biology, NGS, RNA-Seq, Genomics
ASTRID 20150807 [15] Biology, Genomics
Atlas 3.10.1, 3.11.17 [16] Library, Math
Amuse 6.0, 10.0 [17] Astrophysics
ANGSD 20150306, 20150909 [18] Biology, NGS
Affymetrix Power Tools 1.15.0, 1.18.0 [19] Biology, Genomics, Microarray
ARC 20140312 [20] Biology, NGS
Armadillo 6.200.3 [21] Library, C++ , Math
Astral 4.7.6, 4.7.8, 4.7.9 [22] Biology, Bioinformatics, NGS, Phylogenetics
AtomEye 3 [23] Material Science
ATRAM 20140624 [24] Biology, NGS
Augustus 2.6, 3.2.1 [25] Biology, NGS
Auto3DEM 4.05.1 [26] Image Reconstruction
BamBam 1.0 [27] Biology, NGS
Bam-readcount 20150216 [28] Biology, NGS
Bamstats 20140602 [29] Biology, NGS
Bamtools 2.1.1 [30] Biology, NGS
BamUtil 1.0.2 [31] Biology, NGS
Bam-Readcount 20150616 [32]] Biology, Genomics
BAPS 6.0 [33] Biology, Populaton genetics
Basemount 0.1.2.464 [34] Biology, DNA Sequencing
BayesRate 1.3.43 [35] Biology, Phylogenetics
Bbcp 12.08.17.00.0 [36] Network file transfer
Bcbio-nextgen 0.8.7 [37] Biology, NGS
Bcftools 1.0, 1.2 [38] Biology, Genomics, NGS
Bcl2fastq 2.16 [39] Biology, NGS, Illumina
BEAGLE 3.2.2, 4.0 [40] Biology, Genetics, Genotyping
BEAST 1.7.5, 1.8.1, 2.1.3 [41] Biology, Phylogenetics
Bedops 2.4.2 [42] Biology, Bioinformatics, Sequence, NGS
BEDTools 2.17.0, 2.23.0, 2.24.0 [43] Biology, NGS
BEST 2.3 [44] Biology, Phylogenetics
BETA 1.0.5 [45] Biology, NGS
BFAST 0.7.0 [46] Biology, NGS
Bismark 0.7.4, 0.7.7, 0.13.0 [47] Biology, NGS, Methylation
Bioconductor Latest [48] Biology, R, Statistics
BioPerl 1.006901 [49] Biology, Perl
BioPython 1.59 [50] Biology, Python
BLASR 20130815 [51] Biology, NGS
NCBI BLAST 2.2.27, 2.2.28, 2.2.29 [52] Biology, Sequence alignment
Blast2go 2.5.0-20120705 [53] Biology, Annotation
BLAT 20120524 [54] Biology, Sequence alignment
Blender 2.63 [55] Graphics
Boost 1.49.0, 1.53.0, 1.54.0 [56] C++, Library
Bowtie 0.12.9, 1.0.0, 1.1.1 [57] Biology, NGS
Bowtie2 2.2.4, 2.2.5, 2.2.6 [58] Biology, NGS
BPP 1.9.0, 2.2, 3.2 [59] Biology, Phylogenetics
BRANCH 1.8.1 [60] Biology, NGS, Mapping
BRATNextGen 20150505 [61] Biology, Genomics
Bsmap 2.74, 2.87 [62] Biology, NGS, Methylation
Busco 1.1b1 [63] Biology, Genomics
Bwa 0.6.1, 0.7.11, 0.7.12 [64] Biology, NGS
Camino 20140723 [65] Biology, Neuroscience, Imaging
CAP3 20120705 [66] Biology, sequence assembly
CASAVA 1.8.2 [67] Biology, NGS
CD-HIT 4.6, 4.6.4 [68] Biology, Genomics
CDO 1.6.1 [69] Climate
CEAS 1.0.2 [70] Biology, Genomics
CellProfiler 2.0 [71] Biology, Image Analysis
CFITSIO 3.370 [72] Library, C
CGATools 1.6.0.42 [73] Biology, NGS
Charmm 36a3 [74] Simulation, Chemistry
Chartdirector 5.1.0 [75] Graphics
CheckM 1.0.4 [76] Biology, Genomics
Chimera 1.7 [77] Biology, Modeling
ChromEvol 2.0 [78] Biology, Phylogenetics
CIMS 4.1.2 [79] Biology, Genomics
Circos 0.63-pre11 [80] Biology, Visualization
CisGenome 2.0 [81] Biology, Genomics, Peak Calling
Clann 3.2.3 [82] Biology, Phylogenetics
CLHEP 2.2.0.1 [83] High Energy Physics
ClonalFrame 1.1, 1.2 [84] Biology, Genomics, NGS
ClonalFrameML 1.25 [85] Biology, Genomics, NGS
ClustalW 2.1 [86] Biology, Genomics
Cluster3 1.52 [87] Biology, Genomics
Clview 20130402 [88] Biology, Genomics
ClustalO 1.2.0 [89] Biology, Genomics
CMake 2.8.8, 2.9.12.1, 3.1.0 [90] Programming, Build System
CMWP 140518 [91] Biology, Genomics
CNVSeq 20110715 [92] Biology, NGS
Cobrapy 0.3.2 [93] Biology, Metabolomics, Modeling
Coevol 1.3c, 1.4b [94] Biology, Phylogenetics
CoMap 1.4.1 [95] Biology, Genomics
CONCOCT 0.3.1 [96] Biology, Genomics
CoNIFER 0.2.2 [97] Biology, Genomics
Consed 23.0 [98] Biology, Genomics
Coreutils 8.23 [99] GNU Utilities, Computer Science
covNMR 2014 [100] Biochemistry
CPLEX 12.6.5 [101] Optimizer
CUDA 4.2, 5.5 [102] Programming, Graphics
Crux 1.40 [103] Biology, Mass-Spectrometry
Cufflinks 1.3.0, 2.0.2, 2.2.1 [104] Biology, NGS
Cutadapt 1.1, 1.7.1, 1.8.1 [105] Biology, NGS
DAKOTA 5.4.0 [106] Computational Science
DaPars 0.9.0 [107] Biology, NGS, RNA-Seq
DCMTK 3.6.0 [108] Biology, Neuroscience, Imaging
DSSAT 4.5 [109] Biology
DDSCAT 7.3.0 [110] Astrophysics
DDT 4.1.0, 4.2.1 [111] Software
Delft3D 3621 [112] Hydrodynamics, Physics
Desmond 3.0.3.1 [113] Simulation, Biology, Chemistry
DETONATE 1.9 [114] Biology, NGS
Dalton 2011 [115] Quantum Chemistry
Diamond 0.5.1 [116] Computational Biology, Genomics
Dibig Tools 1.0 [117] Bioinformatics, PBS, Torque, Jobs
DiffReps 1.55.4 [118] Biology, NGS, ChIP-Seq
Dindel 1.01 [119] Biology, NGS
DISCOVARdenovo 52488 [120] Biology, NGS
DIYABC 1.0.4.43b, 2.0.3 [121] Biology, Genomics
Dlpoly 4.03.4 [122] Simulation, Biology, Chemistry
Dlpoly-Classic 1.9 [123] Simulation, Biology, Chemistry
DNA Clust 3.0 [124] Biology, Genomics
Dock 6.5, 6.6, 6.7 [125] Chemistry, ligand binding prediction
DOT 2.0 [126] Biology, Bioinformatics, Docking
Doxygen 1.8.3.1 [127] Programming, Documentation
DSSP 2.2.1 [128] Biology, Molecular Dynamics
DTI-TK 2.3.1 [129] Biology, Neurology, Imaging
EA-Utils 1.1.2.537 [130] Biology, NGS
ECTools 20140311, 20141201 [131] Biology, Sequencing, Bioinformatics
EEGLAB 12.0.2.1b, 13.2.2b, 13.4.4b [132] Biology, Matlab
EIGENSOFT 4.2, 5.0.1, 6.0.1 [133] Biology, Population
emboss 6.5.7 [134] Biology, multi-tool suite
EMAN2 2.11 [135] Biology
EMIRGE 20130727 [136] Biology, NGS
Ensembl_Tools 80 [137] Biology, Bioinformatics
EPACTS 3.2.6 [138] Biology, Bioinformatics, Genomics
EPOCH 4.7.3 [139] Astronomy, CPPP
eQTLA 1.1 [140] Biology, Genomics
Eqtlbma 1.2.2 [141] Biology, Genotyping
Esmf 6.3.0rp1 [142] Climate
Espresso 5.0.1, 5.2.0, 5.2.1 [143] Modeling, Physics
ESPRIT 201211 [144] Biology, NGS, Metagenomics
ETE2 2.1 [145] Biology, Phylogenetics
Eval 2.2.8 [146] Biology, Genomics, GUI
ExaBayes 1.2.1, 1.4.1 [147] Biology, Phylogenetics
ExaML 1.0.5, 1.0.12, 3.0.14 [148] Biology, Phylogenetics
ExomeCNV 1.4 [149] Biology, NGS, Genomics
Exonerate 2.2.0 [150] Biology, Genomics
eXpress 1.3.1 [151] Biology, NGS
FAR 2.15 [152] Biology, Genomics
FASTA 34.26.5, 36.3.6d [153] Biology, Genomics
FastML 3.0 [154] Biology, Phylogenetics, ML
FastQC 0.9.6, 0.10.1 [155] Biology, NGS
Fastq-tools 0.7, 0.8 [156] Biology, NGS
FastTree 2.1.7 [157] Biology, Phylogenetics
Fastx_toolkit 0.0.13.2 [158] Biology, NGS
Fathmm 20150225 [159] Biology, Genomics
fcGENE 1.0.7 [160] Biology, Genomics, SNP
Ferret 6.82 [161] Oceanography, Meteorology
FFmpeg 2.1.3, 2.8.3 [162] Multimedia, audio, video
FFTW 3.3.2, 3.3.3 [163] Math, Library, C++
FLASH 1.2.10, 1.2.11 [164] Biology, Genomics, NGS
Flexbar 2.3 [165] Biology, Genomics, NGS
Fluent 14.5.7, 15.0.7, 16.0 [166] Simulation, Fluid Dynamics
FragGeneScan 1.16 [167] Biology, NGS, Genomics
FreeBayes 0.9.15, 0.9.21, 1.0.1 [168] Biology, NGS, SNP Calling
Freesurfer 5.2.0, 5.3.0 [169] Biology, Neurology, Imaging
FSL 5.0.2.2 [170] Biology, Neurology, Imaging
Galaxy latest [171] Biology, Chemistry, Other
GapFiller 1.11 [172] Biology, NGS
Garli 2.0, 2.01 [173] Biology, Phylogenetics
GAML 20150610 [174] Biology, NGS
GARM 0.7.4 [175] Biology, NGS
GASVPro 201310 [176] Biology, NGS, Genomics
GATE 7.0 [177] Data Analysis
GATK 1.6.9, 3.1.1, 3.3.0, 3.4.46 [178] Biology, NGS
Gaussian G03, G09-A.02, G09-C.01 [179] Modeling, Computational Chemistry
Gblocks 0.91b [180] Genomics, Alignment tool
GCTA 1.24.7 [181] Biology, Genomics, SNP
GDAL 1.11.2 [182] Geospatial Data Modeling, Geospatial Library
Geant4 4.10 [183] Physics
GEM 20130406 [184] Biology, NGS
GEMINI 4.6.6a, 0.13.1 [185] Biology, Genomics, Genetics
GenBank Tools 20140130 [186] BIology< Genomics
GeneMark 2012.04 [187] Biology, Genomics, Metagenomics
GeneSeqer 20140226 [188] Biology, Genomics
Genewise 2.2.0 [189] Biology, Genomics, Annotation
Genome STRiP 2.00.1602 [190] Biology, genomics, NGS
GenomicTools 2.7.0 [191] Biology, NGS
GenomeTools 1.5.7 [192] Biology, Bioinformatics
GenSel 4.90 [193] Biology, Genetics
GET_HOMOLOGUES 20150529 [194] Biology, Genomics
GKNO 1.30.18 [195] Biology, NGS,
Git 1.8.2.1, 1.9.0 [196] Development, Revision Control
Globus 2.1.3 [197] Data Transfer
GLPK 4.55 [198] Biology, Genomics
Gmap 20150612, 20150723 [199] Biology, Genomics
GNU 4.4.6, 4.7.2 [200] Compilers, Programming
GnuPlot 4.6.0 [201] Graphics, Plotting, Programming
Grace 5.1.22 [202] Graphics, plotting, 2D
GrADS 2.0.1 [203] Earth Science
GramCluster 1.3 [204] Biology, Sequencing
GraphViz 2.38.0 [205] Graphics, plotting, visualization
Gromacs 4.5.5, 4.6.5 [206] Chemistry, Modeling, Simulation
GSNP 1.0 [207] Biology, Bioinformatics, NGS
GSL 1.15 [208] Library, Math, C++, C
Gsutil 4.15 [209] Cloud, Storage, Google
Gubbins 20150519 [210] Biology, Phylogenetics, Genomics
GULP 4.0 [211] Material Science
HaMStR 13.2.2, 13.2.3, 13.2.4 [212] Biology, Genomics
HapCompass 0.7.7 [213] Biology, NGS, Genomics
Hapsembler 2.21 [214] Biology, Genomics, NGS
HapTree 1.0 [215] Biology, Genomics, NGS
HDF4 4.2.11 [216] Library, Data
HDF5 1.8.9, 1.8.12, 1.8.15 [217] Library, Data
HISAT2 2.0.0b, 2.0.1b [218] Biology, Sequence Alignment, NGS
HMMER3 3.0, 3.1b1, 3.1b2 [219] Biology, Genomics
HMMSplicer 0.9.5 [220] Biology, Genomics
HOMER 4.2 [221] Biology, Genomics
HTMLDoc 1.2.82 [222] Documentation, PDF, HTML
HTSeq 0.5.3p3, 0.6.1p1 [223] Biology, NGS
Hyb 20141126 [224] Biology, NGS, RNA-Seq
HyPhy 2.1.2.28 [225] Biology, Phylogenetics
Hypre 1.10.0b, 2.8.0b [226] Library, Math, Physics
IBDNe 20150815 [227] Biology, NGS
IDBA-UD 1.0.9, 1.1.0, 1.1.1 [228] Biology, NGS
IDBA-MT 1.0 [229] Biology, NGS
IEP 3.6 [230] Programming, Python, Editor
IGB 8.4.1 [231] Biology, Genomics, NGS
iGTP 1.1 [232] Biology, Bioinformatics, Phylogenetics
illumiprocessor 20150803 [233] Biology, Sequencing
IM and IMa 20091217 [234] Biology, Population
IMa2 20120827 [235] Biology, Population
ImageJ 1.48 [236] Image manipulation
ImageMagick 6.8.8-9 [237] Image manipulation
Intel Compilers 11.1, 2012 [238] Programming, Compilers
IOAPI 3.1 [239] Meteorology
Iprscan 4.8 [240] Biology, Genomics
IQ-TREE 1.3.4, 1.3.9, 1.3.10 [241] Biology, Phylogenetics
ITK 4.3.1 [242] Biology, Genomics
ITK-SNAP 3.0.0 [243] Biology, Neuroscience, Imaging
JAGS 3.3.0 [244] Statistics
Java 1.6.0_31, 1.7.0_02, 1.8.0_31 [245] Java Development Kit
Jellyfish 2.1.1 [246] Biology, NGS
JModelTest 2.1.1 [247] Biology, Phylogenetics, Genomics
Julia 0.3.11 [248] Programming, Languages
KaKs 1.2 [249] Biology, Phylogenetics
Kent 20120524 [250] Biology, NGS
Khmer 1.1, 2.0 [251] Biology, NGS
KING 1.4 [252] Biology, Genomics
Kallisto 0.42.3, 0.42.4 [253] Biology, NGS, RNA-Seq
Kmer 1934 [254] Biology, NGS
KmerGenie 1.6741 [255] Biology, NGS, Utilities
Kraken 0.10.4b [256] Biology, Genomics, Phylogenetics
LAMMPS 28Oct12, 30Sep13, 28Jun14,15May15 [257] Molecular Dynamics Simulation
LAMP 2.5 [258] Biology, Genomics
Last 193, 247 [259] Biology, Sequence alignment
Lastz 1.03.02, 1.02.00 [260] Biology, NGS
LDhat 2.2a [261] Biology, Genomics
LIBSVM 3.12 [262] Machine Learning
LIGR 2.05 [263] Biology, Assembly
LSC 0.3, 0.3.1 [264] Biology, NGS, Error correction
Loci 3.3 [265] Fluid Dynamics
LS-DYNA 700, 711, 800 [266] Physics
Lumpy 0.2.1 [267] Biology, SNP
LZO 2.09 [268] Library, Data Compression
MACH 1.0.18 [269] Biology, Genomics
Mach2VCF 20150515 [270] Biology
M5tools 20121126 [271] Biology, Bioinformatics, Genomics
MACS 1.4.2 [272] Biology, ChIP-Seq
mafft 6.903, 7.215, 7.245 [273] Biology, Multiple sequence alignment
Maker 2.10, 2.25b [274] Biology, Annotation, Genomics
MapSplice 2.1.7 [275] Biology, NGS, RNA-Seq
MAPminer 1.1 [276] Biology, Phylogenetics
MassMine 0.9.5, 0.10.0 [277] Data Mining
Maq 0.7.1 [278] Biology, NGS
MARK 2.0.1 [279] Statistics
MarkerMiner 20150429, 20150511 [280] Biology, Genomics
MaSuRCA 2.3.2 [281] Biology, NGS
Matlab 2012a, 2013a, 2014a [282] Math, Simulation, Programming
MATS 2.1.0, 3.0.8, 3.0.9 [283] BIology, NGS
Mauve 2.3.1 [284] Biology, NGS
MaxBin 2.1.1 [285] Biology, NGS
MCarts 1.0.2 [286] Biology, Genomics, Markov models
MCNP 5, 6b2 [287] Physics
MCNPX 2.7.0, 2.7.0-i8 [288] Physics
MEGAN 5.10.3 [289] Biology, NGS
Megraft 1.0.2 [290] Biology, Sequencing
Melting 4.3.1 [291] Biology, Genome, RNA, Folding
Meme 4.8.1 [292] Biology, Motifs, Sequence analysis
Meraculous 2.0.5 [293] Biology, NGS
Mercurial 2.7 [294] Development, Revision Control
Merlin 1.1.2 [295] Biogolgy, SNP
Metabin 1.0 [296] Biology, Metagenomics
MetaCluster 5.0b [297] Biology, Metagenomics
MetaCV 2.3.0 [298] Biology, NGS
METAL 20110325 [299] Biology, Genomics
MetAMOS 1.5.0rc4-20140827 [300] Biology, Bioinformatics, Genomics, Assembly
Metassembler 1.5 [301] Biology, Genomics
MetaVelvet 1.2.01 [302] Biology, NGS
Metaxa2 2.0.2 [303] Biology, NGS
MetaGeneMark 2012.04 [304] Biology, Genomics
Mfold 3.6 [305] Biology, Genomics
MHAP 1.6 [306] Biology, Sequencing
MIA 20130301 [307] Biology, NGS
Midnight Commander 4.6.1 [308] Tools, Utilities
Migrate-n 3.3.0, 3.6.6 [309] Biology, Population
Minimac 1-20130717, 2-20140915, 3-20150727 [310] Biology, Genomics
mira 3.9.18, 4.0.rc1, 4.0.2 [311] Biology, NGS
MISO 0.4.9, 0.5.2, 0.5.3 [312] Biology, NGS
MMSEQ 1.0.8 [313] Biology, NGS
MSMBuilder 2.5.1 [314] Molecular Dynamics
MOABS 1.2.9 [315] Biology, NGS, Genomics
Modeller 9.11, 9.13, 9.14 [316] Biology, Modeling
Molden 5.0 [317] Molecular, electronic structure
MolPro 2012.1p22 [318] Quantum Chemistry, Ab Initio
mosaik 2.1.33, 2.2.3 [319] Biology,NGS
Mothur 1.31.2, 1.36.1 [320] Biology, Microbial Ecology
MOTU 1.1 [321] Biology, Bioinformatics, Genomics
MP-EST 1.4 [322] Biology, Phylogenetics
mpiP 3.4.1 [323] Parallel Computing
MrBayes 3.2.1, 3.2.4, 3.2.5 [324] Biology, Phylogenetics
MRIcron 201306 [325] Biology, MRI, Imaging
MUMmer 3.23 [326] Biology, Genomics
MUSCLE 3.8.31 [327] Biology, Genomics
MuTect 1.1.4, 1.1.7 [328] Biology, Genomics
MutSig 1.4 [329] Biology, Genomics
MZMine 2.14.2, 2.15, 2.17 [330] Biology, Spectroscopy
NAMD 2.9 [331] Simulation, Chemistry, Biology
Nanocorrect 20150727 [332] Biology, NGS
Nanopolish 20150904 [333] Biology
Nbody 6 [334] Astronomy
NCBI C++ Toolkit 12.0.0 [335] Biology, C++, Development
NCL 6.1.2, 6.3.0 [336] Atmosphere Science
NCO 4.2.1, 4.4.3 [337] Data exchange tools
Ncview 2.1.2 [338] Data visualization
NetCDF 3.4.2, 4.2, 4.3 [339] Data exchange, Tools
Newbler 2.7, 2.8, 2.9 [340] Biology, NGS
Newick utils 1.6 [341] Biology, Phylogenetics
Nextallele 20140718 [342] Biology, Genomics
Nexus NCL 2.1.18 [343] Biology, Phylogenetics, Library
ngsCAT 0.1 [344] Biology, Bioinformatics, NGS
ngsTools 20150816 [345] Biology, NGS
NGSUtils 20130722, 20150206 [346] Biology, NGS
Nipype 0.10.0 [347] Biology, Bioinformatics, Neuroscience, Imaging
NMRPipe 7.9 [348] Biology, Biochemistry
Novoalign 2.08.02, 3.00.02 [349] Biology, NGS
NWChem 6.5 [350] Chemistry
Oases 0.2.08 [351] Biology, NGS
Olego 1.1.2, 1.1.5, 1.1.6 [352] Biology, NGS, RNA-Seq
OCaml 4.02.3 [353] Programming Languages, Scripting, Development
Octave 3.6.4 [354] Numerical Computation
Oncotator 1.5.2.0, 1.5.3.0, 1.8.0.0 [355] Biology, Genomics
OpenBabel 2.3.2 [356] Biology, Chemistry
OpenCL 1.1 [357] Programming, Library
OpenCV 2.4.8 [358] Computervision
OpenFOAM 2.1.1 [359] Fluid Dynamics
OpenMM 6.2.0 [360] Quantum Chemistry
OrthoFinder 0.2.5 [361] Biology, Genomics
OrthoMCL 2.0.2, 2.0.3, 2.0.7 [362] Biology, Genomics
p4vasp 0.3.29 [363] Molecular, Electronic Structure
Pacbio 2.2.0, 2.3.0 [364] Biology, Bioinformatics, NGS
Package-GFE 20150701 [365] Biology, Genomics
PALES 122 [366] Physics
PAML 4.7, 4.8a [367] Biology, Phylogenetics
Pandaseq 20140808, 20150627 [368] Biology, Bioinformatics, NGS, Sequencing
PAPI 5.1.0.2 [369] Software, Computing
Parallel 20150122 [370] Programming, Languages
ParaView 4.1.0, 4.2.0, 4.3.0 [371] Data Analysis
PartitionFinder 1.0.1, 1.1.1 [372] Biology, Phylogenetics, Evolution
Parflow v615 [373] Ecology, Modeling
PASA 1.5, 2.0-r20150209 [374] Biology, Genomics
PAUP 4.0b10 [375] Biology, Phylogenetics
PAUDA 1.0.1 [376] Biology, Bioinformatics, Sequence alignment
PBCore 20151201 [377] Biology, Bioinformatics
PBCommand 20151203 [378] Biology, Library
PBJelly 14.7.14, 15.2.20 [379] Biology, Bioinformatics
pbsdrmaa 1.0.17 [380] Libraries, Torque
pbsmrtpipe 20151202 [381] Biology
PeakSplitter 1.0 [382] Biology, Chip-Seq
PEAR 0.9.2, 0.9.6 [383] Biology, NGS
PDT 3.18 [384] Programming, Profiler
Perl 5.16.0 [385] Programming, Language
PerM 0.4.0 [386] Biology, NGS
PETSc 2.3, 3.3 [387] Math, Numerical solvers
Phenix 1.8.1069, 1.10.2155 [388] Crystallography
PHYLDOG 20130418 [389] Biology, Genomics, Phylogenetics
Phyluce 20140427, 20151103 [390] Biology, Phylogenetics
PfamScan 1.3 [391] Biology, Genomics
PHITS 2.52 [392] Physics
PIPE-CLIP 1.1.0 [393] Biology, NGS
Phonopy 1.9.2 [394] Chemistry
PHYLIP 3.696 [395] Biology, Phylogenetics
PhyloBayes 3.3f, 1.4f MPI [396] Biology, Phylogenetics
Phylosift 1.1 [397] Biology, Genomics, Phylogenetics, Taxonomy
PhyML 3.0, 20121109 [398] Biology, Phylogenetics
Picard 1.69, 1.72, 1.80 [399] Biology, NGS
PICRUSt 1.0.0 [400] Biology, Phylogenetics
Piranha 1.2.1 [401] Biology, Phylogenetics
PLAST 1.0 [402] Biology, Bioinformatics
Plink 1.07, 1.90b3 [403] Biology, GWAS
PLINKSEQ 0.10 [404] Biology, Genomics
PluMiST 1.1 [405] Biology, Phylogenetics, Genomics
PolyPhen 2.2.2.r405b [406] Biology, Genomics
Poretools 0.5.0 [407] Biology, Sequencing
POV-Ray 3.7 [408] 3D, Graphics
Preseq 0.0.4 [409] Biology, NGS
Primer3 2.3.4 [410] Biology, Genomics
ProfessAtQE 2014 [411] Material Science, Molecular Dynamics
Prokka 1.10 [412] Biology, Genomics, Bioinformatics, Assembly
ProBABEL 0.4.2, 0.4.3, 0.4.5 [413] Biology, Genomics, GWAS
Probalign 1.4 [414] Biology, Genomics
Proovread 1.03rcl [415] Biology, Genomics, NGS
Proteinortho 4.26 [416] Biology, Genomics
PROVEAN 1.1.5 [417] Biology, Genomics
Python 2.7.6, 3.5.0 [418] Biology, Genomics, NGS
Pyrad 3.0.63 [419] Biology, Sequencing Alignment, Assembly
QDD 3.1.2 [420] Programming, scripting, language
QIIME 1.5.0 [421] Biology, Ecology
QT 4.8.3 [422] Computer Science
QUAST 2.3 [423] Biology, NGS
Quantas 1.0.4, 1.0.8 [424] Biology, Bioinformatics, NGS
QualiMap 2.1.1 [425] Biology, Sequence alignment
Quickquartet 1.0.0 [426] Biology, Phylogenetics
R Rmpi/2.15.1, 3.0.2, 3.2.0 [427] Statistics, Programming
R8S 1.71, 1.8 [428] Biology, Evolution
RADICAL 0.2 [429] Biology, Phylogenetics, Genomics
REAPR 1.0.18 [430] Biology, Bioinformatics, Assembly
RAxML 8.1.23, 8.2.2, 8.2.3 [431] Biology, Phylogenetics
RepeatExplorer 20150506 [432] Biology, Genomics
RepeatMasker 3.3.0 [433] Biology, Genomics
Reptile 1.1 [434] Biology, NGS, error correction
riboPicker 0.4.3 [435] Biology, Sequence
RNAhybrid 2.1.1 [436] Biology, Genomics
ROOT 6.0 [437] Data Analysis
Roary 3.4.1 [438] Biology, Genomics
Rosetta 2014wk4 [439] Biology, Structure, Modelling
RSEG 0.4.8 [440] Biology, NGS
RSEM 1.1.17, 1.2.7, 1.2.19 [441] Biology, NGS, RNA-Seq
RSeQC 2.3.7, 2.6.2 [442] Biology, NGS, RNA-Seq
Ruby 1.9.3-p0 [443] Programming, Scripting, Language
Sailfish 0.6.3 [444] Biology, NGS, RNA-Seq
Sambamba 0.5.0-dev, 0.5.1 [445] Biology, NGS
Samstat 1.08 [446] Biology, NGS, Bioinformatics, Sequencing
Samblaster 0.1.14 [447] Biology, NGS
samtools 1.0, 1.1, 1.2 [448] Biology, NGS
SAS 9.3 [449] Statistics, Graphing
SATe 2.2.7 [450] Biology, Phylogenetics
Scala 2.11.5 [451] Programming, Language
Scalablast 2.4.53 [452] Biology, Genomics
Scalpel 0.1.1 [453] Biology, NGS
SHAPEIT 2.5.5 [454] Biology, SNP
Sharcgs 1.2.11 [455] Biology, NGS, Assembly
Schrodinger 2012, 2013 [456] Simulation, chemistry
SCons 2.3.0 [457] Programming
SCRATCH1D 1.0 [458] Biology, Genomics
Scythe 0.991 [459] Biology, NGS
Segemehl 0.1.9 [460] Biology, NGS, Mapper
SEPP 1.0, 3.0 [461] Biology, Phylogenetics, HMM
Seq-Gen 1.3.3 [462] Biology, Phylogenetics
SeqPrep 0.5 [463] Biology, NGS
SeqMap 1.0.13 [464] Biology, NGS
Seqtk 20140729 [465] Biology, NGS
SEQuel 1.0.1 [466] Biology, NGS
SeqyClean 1.8.10 [467] Biology, NGS, Bioinformatics
ShoRAH 20131204 [468] Biology, NGS, quality filter
SHRiMP 2.2.3 [469] Biology, NGS
Sickle 1.200, 1.33 [470] Biology, NGS, quality filter
Siesta 2.0.2,3.1 [471] Simulation, Physics, Ab Initio
SIFT 4.0.3b [472] Biology, Genomics
Silo 4.7 [473] Library, Data
SIPeS 2.0 [474] Biology, Bioinformatics, ChIP-Seq
Slicer 4.3.1 [475] Biology, Imaging
SMALT 0.7.6 [476] Biology, NGS
Snap 20100728 [477] Biology, Genomics
SNAPE-pooled 20130407 [478] Biology, SNP
SNeP 1.1 [479] Biology, Phylogenics
SnpEff 3.3h, 4.0e, 4.1i [480] Biology, NGS, Genomics
SNPhylo 20140701 [481] Bilogy, Phylogenetics
SOAPdenovo 1.05 [482] Biology, NGS
SOAPdenovo-Trans 1.01, 1.03 [483] Biology, NGS
SOAPsplice 1.10 [484] Biology, NGS
SparCC 201402 [485] Microbial Ecology
Spades 3.5.0, 3.6.0, 3.6.2 [486] Biology, NGS
Spanki 0.4.1, 0.4.3, 0.5.0 [487] Biology, NGS, RNA-Seq
SPARTA+ 2.60 [488] Chemistry
Spidey 20150922 [489] Biology, Genomics
SPIMAP 1.1 [490] Biology, Phylogenetics
SpliceTrap 0.90.5 [491] Biology, NGS, RNA-Seq
SPM 8 [492] Biology, Statistics, Neurology, Imaging
Sputnik 1.0 [493] Biology, Genomics
SQLite 3.8.8.2 [494] Database
SQL_Developer 4.1.2 [495] Programming, Oracle, Sql
SRA 2.1.10 [496] biology, NGS
SSPACE 2.0, 3.0 [497] Biology, NGS
Stacks 1.21, 1.24, 1.35 [498] Biology, Genomics, NGS
STAR 2.3.0e [499] Biology, NGS, Alignment
STAR-CCM+ 8.06 [500] Mechanical Engineering
Stata 10.1, 13 [501] Statistics, Data analysis
Stringtie 0.97, 1.0.0, 1.1.2 [502] Biology, NGS, Alignment
Structure 2.3.3, 2.3.4 [503] Biology, Population
SUNDIALS 2.3.0, 2.5.0 [504] Numerical Solver
SVDetect 0.8b [505] Biology, NGS, SNP
swak4Foam 2.x [506] Fluid Dynamics
swarm 1.2.11 [507] Data Analysis
Swig 2.0.9 [508] Programming, C, C++, Python
SwitchSeq 20140907 [509] Biology, NGS
Syzygy 1.2.7 [510] Biology, Genomics
TASSEL 5.0 [511] Biology, Genomics
TAU 2.21.4, 2.23 [512] Profiling, Tracing, Programming
T-Coffee 9.03.r1318 [513] Biology, Genomics, Multiple Alignment
TESS 2.3.1 [514] Biology, Genomics, Markov
tgicl 2.1 [515] Biology, sequencing, clustering
Tmux 2.0 [516] GNU, Terminal Multiplexer
TomoPy 0.0.3 [517] Biology, Neuroimaging
Tophat 1.4.1, 2.0.13, 2.1.0 [518] Biology, NGS
Torch 20151107 [519] Lua
Totalview 8.12.0 [520] Computer Science
TPP 4.7.0 [521] Bioinformatics, MassSpec
TrackTools 2011 [522] Bioinformatics
TrackVis 0.5.2.2 [523] Biology, Spectroscopy
Tracula 5.3.2014_05_26 [524] Biology, Bioinformatics, Neuroscience, Imaging
TraitRate 1.1 [525] Biology, Evolution
TransDecoder 20140704, 2.0.1 [526] Biology, NGS
Transrate 1.0.1 [527] Biology, Assembly
TreeFix 1.1.7, 1.1.10 [528] Biology, Phylogenetics
TreePL 20150305 [529] Biology, Phylogenetics
TriMetAss 1.1 [530] Biology, Bioinformatics, NGS
TRF 4.04 [531] Biology, Genomics
Trilinos 11.4.1, 11.8.1 [532] Math Algorithm
trimAl 1.2 [533] Biology, Genomics, Sequence Alignment
Trim Galore 0.2.8, 0.4.1 [534] Biology, NGS
Trimmomatic 0.22, 0.32, 0.33 [535] Biology, NGS
Trinity r20150215-2.0.4, r20150302-2.0.6 [536] Biology, NGS, RNA-Seq
Trinotate 2.0.1 [537] Biology
TRNAscan-SE 1.23 [538] Biology, NGS, Bioinformatics
Twinscan 4.1.2 [539] Biology, Genomics
usearch 7.0.1001-64, 8.0.1517 [540] Biology, Sequence analysis
UDUNITS 2.2.17 [541] Library, Units, Programming
UNAFold 3.8 [542] Biology, Genome, RNA, Folding
UProC 1.2.0 [543] Biology, Genomics
Valgrind 3.9.0 [544] Computer Science
VarScan 2.3.6 [545] Biology, NGS, Genomics
VASP 5.3.2, 5.3.3, 5.3.5 [546] Quantum Chemistry, Ab Initio
VAST-TOOLS 20150506 [547] Biology, NGS, RNA-Seq
VCFLib 20141119, 20150313 [548] Biology, NGS, Genomics
VCFtools 0.1.12a, 0.1.12b, 0.1.14 [549] Biology, SNPs
velvet 1.2.06, 1.2.07, 1.2.10 [550] Biology, Genomics, NGS
VEP 74 [551] Biology, NGS
VICUNA 1.3 [552] Biology, Assembly
Vim 7.4.5 [553] Programming, Scripting, Language
vmd 1.9.1 [554] Biology, Visualization
VSearch 20151022 [555] Biology, NGS
VTK 6.1.0 [556] Visualization, Graphics
Wannier90 1.2, 2.0.0 [557] Computational Physics
WebLogo 3.3 [558] Biology, Genomics
WDSSII 1 [559] Meteorology
WIEN2k 12.1 [560] Material Science, Chemistry
Wgs or Celera 8.2, 8.3rc1, 8.3rc1.r4638 [561] Biology, NGS
wublast 2.0 [562] Biology, Sequence Alignment
YAHA 0.1.82 [563] Biology NGS
XCrySDen 1.5.60 [564] Computational Material Science
Yambo 3.3.0 [565] Physics
YASM 1.3.0 [566] Computer Science
Yasra 2.32 [567] Biology, NGS
Zagros 1.0.0 [568] Biology, NGS
  1. ↑ Up to 3 most recent/important releases are listed. See the software wiki pages and the output of "module spider software" for full version listing.

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