Difference between revisions of "Installed Software"

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Line 1,067: Line 1,067:
 
| [[VCFLib]] || 20141119, 20150313 || [https://github.com/ekg/vcflib] || Biology, NGS, Genomics
 
| [[VCFLib]] || 20141119, 20150313 || [https://github.com/ekg/vcflib] || Biology, NGS, Genomics
 
|-
 
|-
−
| [[VCFtools]] || 0.1.11, 0.1.12a, 0.1.12b || [http://vcftools.sourceforge.net/] || Biology, SNPs
+
| [[VCFtools]] || 0.1.12a, 0.1.12b, 0.1.14 || [http://vcftools.sourceforge.net/] || Biology, SNPs
 
|-
 
|-
 
| [[velvet]] || 1.2.06, 1.2.07, 1.2.10 || [http://www.ebi.ac.uk/~zerbino/velvet/] || Biology, Genomics, NGS
 
| [[velvet]] || 1.2.06, 1.2.07, 1.2.10 || [http://www.ebi.ac.uk/~zerbino/velvet/] || Biology, Genomics, NGS

Revision as of 17:08, 9 November 2015

  • Last updated on 2015-11-09.
  • 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
AbInit 6.12.3, 7.10.2, 7.10.4 [1] Quantum Chemistry, DFT
Abyss 1.3.4, 1.3.7, 1.5.2 [2] Biology, NGS
AdmixTools 20150311 [3] Biology, Bioinformatics, Genomics, NGS
ADMIXTURE 1.23 [4] Biology, Bioinformatics, Genomics, NGS
AEGeAn 0.14.0 [5] Biology, Genomics
AFNI 2011_12_21_1014 [6] Biology, Statistics, Imaging, Neurology
Agalma 0.2.1, 0.3.5, 0.5.0 [7] Biology, Bioinformatics, Genomics, SNP
ALE 20150507 [8] Biology, Bioinformatics, Assembly
ALLPATHS-LG 42316, 44837 [9] Biology, NGS
Amber 11, 12, 14 [10] Simulation, chemistry
AMOS 3.1.0 [11] Biology, Genomics, NGS
ANNOVAR 20120621, 20150322 [12] Biology, Genomics
AStalavista 3.2 [13] Biology, NGS, RNA-Seq, Genomics
ASTRID 20150807 [14] Biology, Genomics
Atlas 3.10.1, 3.11.17 [15] Library, Math
Amuse 6.0, 10.0 [16] Astrophysics
ANGSD 20150306, 20150909 [17] Biology, NGS
Affymetrix Power Tools 1.15.0, 1.18.0 [18] Biology, Genomics, Microarray
ARC 20140312 [19] Biology, NGS
Astral 4.7.6, 4.7.8, 4.7.9 [20] Biology, Bioinformatics, NGS, Phylogenetics
AtomEye 3 [21] Material Science
ATRAM 20140624 [22] Biology, NGS
Augustus 2.6 [23] Biology, NGS
Auto3DEM 4.05.1 [24] Image Reconstruction
BamBam 1.0 [25] Biology, NGS
Bam-readcount 20150216 [26] Biology, NGS
Bamstats 20140602 [27] Biology, NGS
Bamtools 2.1.1 [28] Biology, NGS
BamUtil 1.0.2 [29] Biology, NGS
BAPS 6.0 [30] Biology, Populaton genetics
Basemount 0.1.2.464 [31] Biology, DNA Sequencing
BayesRate 1.3.43 [32] Biology, Phylogenetics
Bbcp 12.08.17.00.0 [33] Network file transfer
Bcbio-nextgen 0.8.7 [34] Biology, NGS
Bcftools 1.0, 1.2 [35] Biology, Genomics, NGS
Bcl2fastq 2.16 [36] Biology, NGS, Illumina
BEAGLE 3.2.2, 4.0 [37] Biology, Genetics, Genotyping
BEAST 1.7.5, 1.8.1, 2.1.3 [38] Biology, Phylogenetics
Bedops 2.4.2 [39] Biology, Bioinformatics, Sequence, NGS
BEDTools 2.17.0, 2.23.0, 2.24.0 [40] Biology, NGS
BEST 2.3 [41] Biology, Phylogenetics
BETA 1.0.5 [42] Biology, NGS
BFAST 0.7.0 [43] Biology, NGS
Bismark 0.7.4, 0.7.7, 0.13.0 [44] Biology, NGS, Methylation
Bioconductor Latest [45] Biology, R, Statistics
BioPerl 1.006901 [46] Biology, Perl
BioPython 1.59 [47] Biology, Python
BLASR 20130815 [48] Biology, NGS
NCBI BLAST 2.2.27, 2.2.28, 2.2.29 [49] Biology, Sequence alignment
Blast2go 2.5.0-20120705 [50] Biology, Annotation
BLAT 20120524 [51] Biology, Sequence alignment
Blender 2.63 [52] Graphics
Boost 1.49.0, 1.53.0, 1.54.0 [53] C++, Library
Bowtie 0.12.9, 1.0.0, 1.1.1 [54] Biology, NGS
Bowtie2 2.2.4, 2.2.5, 2.2.6 [55] Biology, NGS
BPP 2.2, 1.9.0 [56] Biology, Phylogenetics
BRANCH 1.8.1 [57] Biology, NGS, Mapping
BRATNextGen 20150505 [58] Biology, Genomics
Bsmap 2.74, 2.87 [59] Biology, NGS, Methylation
Bwa 0.6.1, 0.7.11, 0.7.12 [60] Biology, NGS
Camino 20140723 [61] Biology, Neuroscience, Imaging
CAP3 20120705 [62] Biology, sequence assembly
CASAVA 1.8.2 [63] Biology, NGS
CD-HIT 4.6, 4.6.4 [64] Biology, Genomics
CDO 1.6.1 [65] Climate
CEAS 1.0.2 [66] Biology, Genomics
CellProfiler 2.0 [67] Biology, Image Analysis
CGATools 1.6.0.42 [68] Biology, NGS
Charmm 36a3 [69] Simulation, Chemistry
Chartdirector 5.1.0 [70] Graphics
CheckM 1.0.4 [71] Biology, Genomics
Chimera 1.7 [72] Biology, Modeling
ChromEvol 2.0 [73] Biology, Phylogenetics
CIMS 4.1.2 [74] Biology, Genomics
Circos 0.63-pre11 [75] Biology, Visualization
CisGenome 2.0 [76] Biology, Genomics, Peak Calling
Clann 3.2.3 [77] Biology, Phylogenetics
CLHEP 2.2.0.1 [78] High Energy Physics
ClonalFrame 1.1, 1.2 [79] Biology, Genomics, NGS
ClonalFrameML 1.25 [80] Biology, Genomics, NGS
ClustalW 2.1 [81] Biology, Genomics
Cluster3 1.52 [82] Biology, Genomics
Clview 20130402 [83] Biology, Genomics
ClustalO 1.2.0 [84] Biology, Genomics
CMake 2.8.8, 2.9.12.1, 3.1.0 [85] Programming, Build System
CNVSeq 20110715 [86] Biology, NGS
Cobrapy 0.3.2 [87] Biology, Metabolomics, Modeling
Coevol 1.3c, 1.4b [88] Biology, Phylogenetics
CoMap 1.4.1 [89] Biology, Genomics
CONCOCT 0.3.1 [90] Biology, Genomics
CoNIFER 0.2.2 [91] Biology, Genomics
Consed 23.0 [92] Biology, Genomics
Coreutils 8.23 [93] GNU Utilities, Computer Science
covNMR 2014 [94] Biochemistry
CPLEX 12.6.5 [95] Optimizer
CUDA 4.2, 5.5 [96] Programming, Graphics
Crux 1.40 [97] Biology, Mass-Spectrometry
Cufflinks 1.3.0, 2.0.2, 2.2.1 [98] Biology, NGS
Cutadapt 1.1, 1.7.1, 1.8.1 [99] Biology, NGS
DAKOTA 5.4.0 [100] Computational Science
DaPars 0.9.0 [101] Biology, NGS, RNA-Seq
DCMTK 3.6.0 [102] Biology, Neuroscience, Imaging
DSSAT 4.5 [103] Biology
DDSCAT 7.3.0 [104] Astrophysics
DDT 4.1.0, 4.2.1 [105] Software
Delft3D 3621 [106] Hydrodynamics, Physics
Desmond 3.0.3.1 [107] Simulation, Biology, Chemistry
DETONATE 1.9 [108] Biology, NGS
Dalton 2011 [109] Quantum Chemistry
Diamond 0.5.1 [110] Computational Biology, Genomics
Dibig Tools 1.0 [111] Bioinformatics, PBS, Torque, Jobs
DiffReps 1.55.4 [112] Biology, NGS, ChIP-Seq
Dindel 1.01 [113] Biology, NGS
DISCOVARdenovo 52488 [114] Biology, NGS
DIYABC 1.0.4.43b, 2.0.3 [115] Biology, Genomics
Dlpoly 4.03.4 [116] Simulation, Biology, Chemistry
Dlpoly-Classic 1.9 [117] Simulation, Biology, Chemistry
DNA Clust 3.0 [118] Biology, Genomics
Dock 6.5, 6.6, 6.7 [119] Chemistry, ligand binding prediction
DOT 2.0 [120] Biology, Bioinformatics, Docking
Doxygen 1.8.3.1 [121] Programming, Documentation
DSSP 2.2.1 [122] Biology, Molecular Dynamics
DTI-TK 2.3.1 [123] Biology, Neurology, Imaging
EA-Utils 1.1.2.537 [124] Biology, NGS
ECTools 20140311, 20141201 [125] Biology, Sequencing, Bioinformatics
EEGLAB 12.0.2.1b, 13.2.2b, 13.4.4b [126] Biology, Matlab
EIGENSOFT 4.2, 5.0.1, 6.0.1 [127] Biology, Population
emboss 6.5.7 [128] Biology, multi-tool suite
EMAN2 2.11 [129] Biology
EMIRGE 20130727 [130] Biology, NGS
Ensembl_Tools 80 [131] Biology, Bioinformatics
EPACTS 3.2.6 [132] Biology, Bioinformatics, Genomics
eQTLA 1.1 [133] Biology, Genomics
Eqtlbma 1.2.2 [134] Biology, Genotyping
Esmf 6.3.0rp1 [135] Climate
Espresso 5.0.1, 5.2.0, 5.2.1 [136] Modeling, Physics
ESPRIT 201211 [137] Biology, NGS, Metagenomics
ETE2 2.1 [138] Biology, Phylogenetics
Eval 2.2.8 [139] Biology, Genomics, GUI
ExaBayes 1.2.1 [140] Biology, Phylogenetics
ExaML 1.0.5, 1.0.12, 3.0.14 [141] Biology, Phylogenetics
ExomeCNV 1.4 [142] Biology, NGS, Genomics
Exonerate 2.2.0 [143] Biology, Genomics
eXpress 1.3.1 [144] Biology, NGS
FAR 2.15 [145] Biology, Genomics
FASTA 34.26.5, 36.3.6d [146] Biology, Genomics
FastML 3.0 [147] Biology, Phylogenetics, ML
FastQC 0.9.6, 0.10.1 [148] Biology, NGS
Fastq-tools 0.7, 0.8 [149] Biology, NGS
FastTree 2.1.7 [150] Biology, Phylogenetics
Fastx_toolkit 0.0.13.2 [151] Biology, NGS
Fathmm 20150225 [152] Biology, Genomics
fcGENE 1.0.7 [153] Biology, Genomics, SNP
Ferret 6.82 [154] Oceanography, Meteorology
FFmpeg 2.1.3 [155] Multimedia, audio, video
FFTW 3.3.2, 3.3.3 [156] Math, Library, C++
FLASH 1.2.10, 1.2.11 [157] Biology, Genomics, NGS
Flexbar 2.3 [158] Biology, Genomics, NGS
Fluent 14.5.7, 15.0.7, 16.0 [159] Simulation, Fluid Dynamics
FragGeneScan 1.16 [160] Biology, NGS, Genomics
FreeBayes 0.9.6, 0.9.15, 0.9.21 [161] Biology, NGS, SNP Calling
Freesurfer 5.2.0 [162] Biology, Neurology, Imaging
FSL 5.0.2.2 [163] Biology, Neurology, Imaging
Galaxy latest [164] Biology, Chemistry, Other
GapFiller 1.11 [165] Biology, NGS
Garli 2.0, 2.01 [166] Biology, Phylogenetics
GAML 20150610 [167] Biology, NGS
GARM 0.7.4 [168] Biology, NGS
GASVPro 201310 [169] Biology, NGS, Genomics
GATE 7.0 [170] Data Analysis
GATK 1.6.9, 3.1.1, 3.3.0, 3.4.46 [171] Biology, NGS
Gaussian G03, G09-A.02, G09-C.01 [172] Modeling, Computational Chemistry
Gblocks 0.91b [173] Genomics, Alignment tool
GCTA 1.24.7 [174] Biology, Genomics, SNP
GDAL 1.11.2 [175] Geospatial Data Modeling, Geospatial Library
Geant4 4.10 [176] Physics
GEM 20130406 [177] Biology, NGS
GEMINI 4.6.6a, 0.13.1 [178] Biology, Genomics, Genetics
GenBank Tools 20140130 [179] BIology< Genomics
GeneMark 2012.04 [180] Biology, Genomics, Metagenomics
GeneSeqer 20140226 [181] Biology, Genomics
Genewise 2.2.0 [182] Biology, Genomics, Annotation
Genome STRiP 2.00.1602 [183] Biology, genomics, NGS
GenomicTools 2.7.0 [184] Biology, NGS
GenSel 4.90 [185] Biology, Genetics
GET_HOMOLOGUES 20150529 [186] Biology, Genomics
GKNO 1.30.18 [187] Biology, NGS,
Git 1.8.2.1, 1.9.0 [188] Development, Revision Control
Globus 2.1.3 [189] Data Transfer
GLPK 4.55 [190] Biology, Genomics
Gmap 20150612, 20150723 [191] Biology, Genomics
GNU 4.4.6, 4.7.2 [192] Compilers, Programming
GnuPlot 4.6.0 [193] Graphics, Plotting, Programming
Grace 5.1.22 [194] Graphics, plotting, 2D
GrADS 2.0.1 [195] Earth Science
GramCluster 1.3 [196] Biology, Sequencing
GraphViz 2.38.0 [197] Graphics, plotting, visualization
Gromacs 4.5.5, 4.6.5 [198] Chemistry, Modeling, Simulation
GSNP 1.0 [199] Biology, Bioinformatics, NGS
GSL 1.15 [200] Library, Math, C++, C
Gsutil 4.15 [201] Cloud, Storage, Google
Gubbins 20150519 [202] Biology, Phylogenetics, Genomics
GULP 4.0 [203] Material Science
HaMStR 13.2.2, 13.2.3, 13.2.4 [204] Biology, Genomics
HapCompass 0.7.7 [205] Biology, NGS, Genomics
Hapsembler 2.21 [206] Biology, Genomics, NGS
HapTree 1.0 [207] Biology, Genomics, NGS
HDF4 4.2.11 [208] Library, Data
HDF5 1.8.9, 1.8.12, 1.8.15 [209] Library, Data
HMMER3 3.0, 3.1b1, 3.1b2 [210] Biology, Genomics
HMMSplicer 0.9.5 [211] Biology, Genomics
HOMER 4.2 [212] Biology, Genomics
HTMLDoc 1.2.82 [213] Documentation, PDF, HTML
HTSeq 0.5.3p3, 0.6.1p1 [214] Biology, NGS
Hyb 20141126 [215] Biology, NGS, RNA-Seq
HyPhy 2.1.2.28 [216] Biology, Phylogenetics
Hypre 1.10.0b, 2.8.0b [217] Library, Math, Physics
IBDNe 20150815 [218] Biology, NGS
IDBA-UD 1.0.9, 1.1.0, 1.1.1 [219] Biology, NGS
IEP 3.6 [220] Programming, Python, Editor
IGB 8.4.1 [221] Biology, Genomics, NGS
iGTP 1.1 [222] Biology, Bioinformatics, Phylogenetics
IM and IMa 20091217 [223] Biology, Population
IMa2 20120827 [224] Biology, Population
ImageJ 1.48 [225] Image manipulation
ImageMagick 6.8.8-9 [226] Image manipulation
Intel Compilers 11.1, 2012 [227] Programming, Compilers
IOAPI 3.1 [228] Meteorology
Iprscan 4.8 [229] Biology, Genomics
IQ-TREE 1.3.4, 1.3.9 [230] Biology, Phylogenetics
ITK 4.3.1 [231] Biology, Genomics
ITK-SNAP 3.0.0 [232] Biology, Neuroscience, Imaging
JAGS 3.3.0 [233] Statistics
Java 1.6.0_31, 1.7.0_02, 1.8.0_31 [234] Java Development Kit
Jellyfish 2.1.1 [235] Biology, NGS
JModelTest 2.1.1 [236] Biology, Phylogenetics, Genomics
Julia 0.3.11 [237] Programming, Languages
KaKs 1.2 [238] Biology, Phylogenetics
Kent 20120524 [239] Biology, NGS
Khmer 1.1, 2.0 [240] Biology, NGS
KING 1.4 [241] Biology, Genomics
Kallisto 0.42.3 [242] Biology, NGS, RNA-Seq
Kmer 1934 [243] Biology, NGS
KmerGenie 1.6741 [244] Biology, NGS, Utilities
Kraken 0.10.4b [245] Biology, Genomics, Phylogenetics
LAMMPS 28Oct12, 30Sep13, 28Jun14,15May15 [246] Molecular Dynamics Simulation
LAMP 2.5 [247] Biology, Genomics
Last 193, 247 [248] Biology, Sequence alignment
Lastz 1.03.02, 1.02.00 [249] Biology, NGS
LDhat 2.2a [250] Biology, Genomics
LIBSVM 3.12 [251] Machine Learning
LSC 0.3, 0.3.1 [252] Biology, NGS, Error correction
Loci 3.3 [253] Fluid Dynamics
LS-DYNA 700, 711, 800 [254] Physics
Lumpy 0.2.1 [255] Biology, SNP
LZO 2.09 [256] Library, Data Compression
MACH 1.0.18 [257] Biology, Genomics
Mach2VCF 20150515 [258] Biology
M5tools 20121126 [259] Biology, Bioinformatics, Genomics
MACS 1.4.2 [260] Biology, ChIP-Seq
mafft 6.903, 7.215, 7.245 [261] Biology, Multiple sequence alignment
Maker 2.10, 2.25b [262] Biology, Annotation, Genomics
MapSplice 2.1.7 [263] Biology, NGS, RNA-Seq
MAPminer 1.1 [264] Biology, Phylogenetics
MassMine 0.9.5, 0.10.0 [265] Data Mining
Maq 0.7.1 [266] Biology, NGS
MARK 2.0.1 [267] Statistics
MarkerMiner 20150429, 20150511 [268] Biology, Genomics
MaSuRCA 2.3.2 [269] Biology, NGS
Matlab 2012a, 2013a, 2014a [270] Math, Simulation, Programming
MATS 2.1.0, 3.0.8, 3.0.9 [271] BIology, NGS
Mauve 2.3.1 [272] Biology, NGS
MCarts 1.0.2 [273] Biology, Genomics, Markov models
MCNP 5, 6b2 [274] Physics
MCNPX 2.7.0, 2.7.0-i8 [275] Physics
MEGAN 5.10.3 [276] Biology, NGS
Megraft 1.0.2 [277] Biology, Sequencing
Melting 4.3.1 [278] Biology, Genome, RNA, Folding
Meme 4.8.1 [279] Biology, Motifs, Sequence analysis
Meraculous 2.0.5 [280] Biology, NGS
Mercurial 2.7 [281] Development, Revision Control
Merlin 1.1.2 [282] Biogolgy, SNP
Metabin 1.0 [283] Biology, Metagenomics
MetaCluster 5.0b [284] Biology, Metagenomics
MetaCV 2.3.0 [285] Biology, NGS
METAL 20110325 [286] Biology, Genomics
MetAMOS 1.5.0rc4-20140827 [287] Biology, Bioinformatics, Genomics, Assembly
Metassembler 1.5 [288] Biology, Genomics
MetaVelvet 1.2.01 [289] Biology, NGS
Metaxa2 2.0.2 [290] Biology, NGS
MetaGeneMark 2012.04 [291] Biology, Genomics
Mfold 3.6 [292] Biology, Genomics
MIA 20130301 [293] Biology, NGS
Midnight Commander 4.6.1 [294] Tools, Utilities
Migrate-n 3.3.0, 3.6.6 [295] Biology, Population
Minimac 1-20130717, 2-20140915, 3-20150727 [296] Biology, Genomics
mira 3.9.18, 4.0.rc1, 4.0.2 [297] Biology, NGS
MISO 0.4.9, 0.5.2, 0.5.3 [298] Biology, NGS
MMSEQ 1.0.8 [299] Biology, NGS
MSMBuilder 2.5.1 [300] Molecular Dynamics
MOABS 1.2.9 [301] Biology, NGS, Genomics
Modeller 9.11, 9.13, 9.14 [302] Biology, Modeling
Molden 5.0 [303] Molecular, electronic structure
MolPro 2012.1p22 [304] Quantum Chemistry, Ab Initio
mosaik 2.1.33, 2.2.3 [305] Biology,NGS
Mothur 1.31.2, 1.36.1 [306] Biology, Microbial Ecology
MOTU 1.1 [307] Biology, Bioinformatics, Genomics
MP-EST 1.4 [308] Biology, Phylogenetics
mpiP 3.4.1 [309] Parallel Computing
MrBayes 3.2.1, 3.2.4, 3.2.5 [310] Biology, Phylogenetics
MRIcron 201306 [311] Biology, MRI, Imaging
MUMmer 3.23 [312] Biology, Genomics
MUSCLE 3.8.31 [313] Biology, Genomics
MuTect 1.1.4, 1.1.7 [314] Biology, Genomics
MutSig 1.4 [315] Biology, Genomics
MZMine 2.14.2, 2.15, 2.17 [316] Biology, Spectroscopy
NAMD 2.9 [317] Simulation, Chemistry, Biology
Nanocorrect 20150727 [318] Biology, NGS
Nanopolish 20150904 [319] Biology
Nbody 6 [320] Astronomy
NCBI C++ Toolkit 12.0.0 [321] Biology, C++, Development
NCL 6.1.2 [322] Atmosphere Science
NCO 4.2.1, 4.4.3 [323] Data exchange tools
Ncview 2.1.2 [324] Data visualization
NetCDF 3.4.2, 4.2, 4.3 [325] Data exchange, Tools
Newbler 2.7, 2.8, 2.9 [326] Biology, NGS
Newick utils 1.6 [327] Biology, Phylogenetics
Nextallele 20140718 [328] Biology, Genomics
Nexus NCL 2.1.18 [329] Biology, Phylogenetics, Library
ngsCAT 0.1 [330] Biology, Bioinformatics, NGS
ngsTools 20150816 [331] Biology, NGS
NGSUtils 20130722, 20150206 [332] Biology, NGS
Nipype 0.10.0 [333] Biology, Bioinformatics, Neuroscience, Imaging
NMRPipe 7.9 [334] Biology, Biochemistry
Novoalign 2.08.02, 3.00.02 [335] Biology, NGS
NWChem 6.5 [336] Chemistry
Oases 0.2.08 [337] Biology, NGS
Olego 1.1.2, 1.1.5, 1.1.6 [338] Biology, NGS, RNA-Seq
OCaml 4.02.3 [339] Programming Languages, Scripting, Development
Octave 3.6.4 [340] Numerical Computation
Oncotator 1.5.2.0, 1.5.3.0, 1.8.0.0 [341] Biology, Genomics
OpenBabel 2.3.2 [342] Biology, Chemistry
OpenCL 1.1 [343] Programming, Library
OpenCV 2.4.8 [344] Computervision
OpenFOAM 2.1.1 [345] Fluid Dynamics
OpenMM 6.2.0 [346] Quantum Chemistry
OrthoFinder 0.2.5 [347] Biology, Genomics
OrthoMCL 2.0.2, 2.0.3, 2.0.7 [348] Biology, Genomics
p4vasp 0.3.29 [349] Molecular, Electronic Structure
Pacbio 2.2.0, 2.3.0 [350] Biology, Bioinformatics, NGS
Package-GFE 20150701 [351] Biology, Genomics
PALES 122 [352] Physics
PAML 4.7, 4.8a [353] Biology, Phylogenetics
Pandaseq 20140808, 20150627 [354] Biology, Bioinformatics, NGS, Sequencing
PAPI 5.1.0.2 [355] Software, Computing
Parallel 20150122 [356] Programming, Languages
ParaView 4.1.0, 4.2.0, 4.3.0 [357] Data Analysis
PartitionFinder 1.0.1, 1.1.1 [358] Biology, Phylogenetics, Evolution
Parflow v615 [359] Ecology, Modeling
PASA 1.5, 2.0-r20150209 [360] Biology, Genomics
PAUP 4.0b10 [361] Biology, Phylogenetics
PAUDA 1.0.1 [362] Biology, Bioinformatics, Sequence alignment
PBJelly 14.7.14, 15.2.20 [363] Biology, Bioinformatics
pbsdrmaa 1.0.17 [364] Libraries, Torque
PeakSplitter 1.0 [365] Biology, Chip-Seq
PEAR 0.9.2, 0.9.6 [366] Biology, NGS
PDT 3.18 [367] Programming, Profiler
Perl 5.16.0 [368] Programming, Language
PerM 0.4.0 [369] Biology, NGS
PETSc 2.3, 3.3 [370] Math, Numerical solvers
Phenix 1.8.1069, 1.10.2155 [371] Crystallography
PHYLDOG 20130418 [372] Biology, Genomics, Phylogenetics
Phyluce c561dd9 [373] Biology, Phylogenetics
PfamScan 1.3 [374] Biology, Genomics
PHITS 2.52 [375] Physics
Phonopy 1.9.2 [376] Chemistry
PHYLIP 3.696 [377] Biology, Phylogenetics
PhyloBayes 3.3f, 1.4f MPI [378] Biology, Phylogenetics
Phylosift 1.1 [379] Biology, Genomics, Phylogenetics, Taxonomy
PhyML 3.0, 20121109 [380] Biology, Phylogenetics
Picard 1.69, 1.72, 1.80 [381] Biology, NGS
PICRUSt 1.0.0 [382] Biology, Phylogenics
PLAST 1.0 [383] Biology, Bioinformatics
Plink 1.07, 1.90b3 [384] Biology, GWAS
PLINKSEQ 0.10 [385] Biology, Genomics
PluMiST 1.1 [386] Biology, Phylogenetics, Genomics
PolyPhen 2.2.2.r405b [387] Biology, Genomics
Poretools 0.5.0 [388] Biology, Sequencing
POV-Ray 3.7 [389] 3D, Graphics
Preseq 0.0.4 [390] Biology, NGS
Primer3 2.3.4 [391] Biology, Genomics
ProfessAtQE 2014 [392] Material Science, Molecular Dynamics
Prokka 1.10 [393] Biology, Genomics, Bioinformatics, Assembly
ProBABEL 0.4.2, 0.4.3, 0.4.5 [394] Biology, Genomics, GWAS
Probalign 1.4 [395] Biology, Genomics
Proovread 1.03rcl [396] Biology, Genomics, NGS
Proteinortho 4.26 [397] Biology, Genomics
PROVEAN 1.1.5 [398] Biology, Genomics
Python 2.7.6, 3.5.0 [399] Biology, Genomics, NGS
Pyrad 3.0.63 [400] Biology, Sequencing Alignment, Assembly
QDD 3.1.2 [401] Programming, scripting, language
QIIME 1.5.0 [402] Biology, Ecology
QT 4.8.3 [403] Computer Science
QUAST 2.3 [404] Biology, NGS
Quantas 1.0.4, 1.0.8 [405] Biology, Bioinformatics, NGS
QualiMap 2.1.1 [406] Biology, Sequence alignment
Quickquartet 1.0.0 [407] Biology, Phylogenetics
R Rmpi/2.15.1, 3.0.2, 3.2.0 [408] Statistics, Programming
R8S 1.71, 1.8 [409] Biology, Evolution
RADICAL 0.2 [410] Biology, Phylogenetics, Genomics
REAPR 1.0.18 [411] Biology, Bioinformatics, Assembly
RAxML 8.1.23, 8.2.2, 8.2.3 [412] Biology, Phylogenetics
RepeatExplorer 20150506 [413] Biology, Genomics
RepeatMasker 3.3.0 [414] Biology, Genomics
Reptile 1.1 [415] Biology, NGS, error correction
riboPicker 0.4.3 [416] Biology, Sequence
RNAhybrid 2.1.1 [417] Biology, Genomics
ROOT 6.0 [418] Data Analysis
Roary 3.4.1 [419] Biology, Genomics
Rosetta 2014wk4 [420] Biology, Structure, Modelling
RSEG 0.4.8 [421] Biology, NGS
RSEM 1.1.17, 1.2.7, 1.2.19 [422] Biology, NGS, RNA-Seq
RSeQC 2.3.7, 2.6.2 [423] Biology, NGS, RNA-Seq
Ruby 1.9.3-p0 [424] Programming, Scripting, Language
Sailfish 0.6.3 [425] Biology, NGS, RNA-Seq
Sambamba 0.5.0-dev, 0.5.1 [426] Biology, NGS
Samstat 1.08 [427] Biology, NGS, Bioinformatics, Sequencing
Samblaster 0.1.14 [428] Biology, NGS
samtools 1.0, 1.1, 1.2 [429] Biology, NGS
SAS 9.3 [430] Statistics, Graphing
SATe 2.2.7 [431] Biology, Phylogenetics
Scala 2.11.5 [432] Programming, Language
Scalablast 2.4.53 [433] Biology, Genomics
Scalpel 0.1.1 [434] Biology, NGS
SHAPEIT 2.5.5 [435] Biology, SNP
Sharcgs 1.2.11 [436] Biology, NGS, Assembly
Schrodinger 2012, 2013 [437] Simulation, chemistry
SCons 2.3.0 [438] Programming
SCRATCH1D 1.0 [439] Biology, Genomics
Scythe 0.991 [440] Biology, NGS
Segemehl 0.1.9 [441] Biology, NGS, Mapper
SEPP 1.0, 3.0 [442] Biology, Phylogenetics, HMM
Seq-Gen 1.3.3 [443] Biology, Phylogenetics
SeqPrep 0.5 [444] Biology, NGS
SeqMap 1.0.13 [445] Biology, NGS
Seqtk 20140729 [446] Biology, NGS
SEQuel 1.0.1 [447] Biology, NGS
SeqyClean 1.8.10 [448] Biology, NGS, Bioinformatics
ShoRAH 20131204 [449] Biology, NGS, quality filter
SHRiMP 2.2.3 [450] Biology, NGS
Sickle 1.200, 1.33 [451] Biology, NGS, quality filter
Siesta 2.0.2,3.1 [452] Simulation, Physics, Ab Initio
SIFT 4.0.3b [453] Biology, Genomics
Silo 4.7 [454] Library, Data
SIPeS 2.0 [455] Biology, Bioinformatics, ChIP-Seq
Slicer 4.3.1 [456] Biology, Imaging
SMALT 0.7.6 [457] Biology, NGS
Snap 20100728 [458] Biology, Genomics
SNAPE-pooled 20130407 [459] Biology, SNP
SNeP 1.1 [460] Biology, Phylogenics
SnpEff 3.3h, 4.0e, 4.1i [461] Biology, NGS, Genomics
SNPhylo 20140701 [462] Bilogy, Phylogenetics
SOAPdenovo 1.05 [463] Biology, NGS
SOAPdenovo-Trans 1.01, 1.03 [464] Biology, NGS
SOAPsplice 1.10 [465] Biology, NGS
SparCC 201402 [466] Microbial Ecology
Spades 3.1.0, 3.5.0, 3.6.0 [467] Biology, NGS
Spanki 0.4.1, 0.4.3, 0.5.0 [468] Biology, NGS, RNA-Seq
SPARTA+ 2.60 [469] Chemistry
Spidey 20150922 [470] Biology, Genomics
SPIMAP 1.1 [471] Biology, Phylogenetics
SpliceTrap 0.90.5 [472] Biology, NGS, RNA-Seq
SPM 8 [473] Biology, Statistics, Neurology, Imaging
Sputnik 1.0 [474] Biology, Genomics
SQLite 3.8.8.2 [475] Database
SQL_Developer 4.1.2 [476] Programming, Oracle, Sql
SRA 2.1.10 [477] biology, NGS
SSPACE 2.0, 3.0 [478] Biology, NGS
Stacks 0.9995 [479] Biology, Genomics, NGS
STAR 2.3.0e [480] Biology, NGS, Alignment
STAR-CCM+ 8.06 [481] Mechanical Engineering
Stata 10.1, 13 [482] Statistics, Data analysis
Stringtie 0.97 [483] Biology, NGS, Alignment
Structure 2.3.3, 2.3.4 [484] Biology, Population
SUNDIALS 2.3.0, 2.5.0 [485] Numerical Solver
SVDetect 0.8b [486] Biology, NGS, SNP
swak4Foam 2.x [487] Fluid Dynamics
swarm 1.2.11 [488] Data Analysis
Swig 2.0.9 [489] Programming, C, C++, Python
SwitchSeq 20140907 [490] Biology, NGS
Syzygy 1.2.7 [491] Biology, Genomics
TASSEL 5.0 [492] Biology, Genomics
TAU 2.21.4, 2.23 [493] Profiling, Tracing, Programming
T-Coffee 9.03.r1318 [494] Biology, Genomics, Multiple Alignment
TESS 2.3.1 [495] Biology, Genomics, Markov
tgicl 2.1 [496] Biology, sequencing, clustering
Tmux 2.0 [497] GNU, Terminal Multiplexer
TomoPy 0.0.3 [498] Biology, Neuroimaging
Tophat 1.4.1, 2.0.13, 2.1.0 [499] Biology, NGS
Totalview 8.12.0 [500] Computer Science
TPP 4.7.0 [501] Bioinformatics, MassSpec
TrackTools 2011 [502] Bioinformatics
TrackVis 0.5.2.2 [503] Biology, Spectroscopy
Tracula 5.3.2014_05_26 [504] Biology, Bioinformatics, Neuroscience, Imaging
TraitRate 1.1 [505] Biology, Evolution
TransDecoder 20140704, 2.0.1 [506] Biology, NGS
Transrate 1.0.1 [507] Biology, Assembly
TreeFix 1.1.7, 1.1.10 [508] Biology, Phylogenetics
TreePL 20150305 [509] Biology, Phylogenetics
TRF 4.04 [510] Biology, Genomics
Trilinos 11.4.1, 11.8.1 [511] Math Algorithm
trimAl 1.2 [512] Biology, Genomics, Sequence Alignment
Trim Galore 0.2.8 [513] Biology, NGS
Trimmomatic 0.22, 0.32 [514] Biology, NGS
Trinity r20150215-2.0.4, r20150302-2.0.6 [515] Biology, NGS, RNA-Seq
Trinotate 2.0.1 [516] Biology
TRNAscan-SE 1.23 [517] Biology, NGS, Bioinformatics
Twinscan 4.1.2 [518] Biology, Genomics
usearch 7.0.1001-64, 8.0.1517 [519] Biology, Sequence analysis
UDUNITS 2.2.17 [520] Library, Units, Programming
UNAFold 3.8 [521] Biology, Genome, RNA, Folding
UProC 1.2.0 [522] Biology, Genomics
Valgrind 3.9.0 [523] Computer Science
VarScan 2.3.6 [524] Biology, NGS, Genomics
VASP 5.3.2, 5.3.3, 5.3.5 [525] Quantum Chemistry, Ab Initio
VAST-TOOLS 20150506 [526] Biology, NGS, RNA-Seq
VCFLib 20141119, 20150313 [527] Biology, NGS, Genomics
VCFtools 0.1.12a, 0.1.12b, 0.1.14 [528] Biology, SNPs
velvet 1.2.06, 1.2.07, 1.2.10 [529] Biology, Genomics, NGS
VEP 74 [530] Biology, NGS
VICUNA 1.3 [531] Biology, Assembly
Vim 7.4.5 [532] Programming, Scripting, Language
vmd 1.9.1 [533] Biology, Visualization
VSearch 20151022 [534] Biology, NGS
VTK 6.1.0 [535] Visualization, Graphics
Wannier90 1.2, 2.0.0 [536] Computational Physics
WebLogo 3.3 [537] Biology, Genomics
WDSSII 1 [538] Meteorology
WIEN2k 12.1 [539] Material Science, Chemistry
Wgs or Celera 8.2, 8.3rc1, 8.3rc1.r4638 [540] Biology, NGS
wublast 2.0 [541] Biology, Sequence Alignment
YAHA 0.1.82 [542] Biology NGS
XCrySDen 1.5.60 [543] Computational Material Science
Yambo 3.3.0 [544] Physics
YASM 1.3.0 [545] Computer Science
Yasra 2.32 [546] 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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