Installed Software

• Last updated on 2015-11-10.
• 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	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, 3.2.1	[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
Busco	1.1b1	[60]	Biology, Genomics
Bwa	0.6.1, 0.7.11, 0.7.12	[61]	Biology, NGS
Camino	20140723	[62]	Biology, Neuroscience, Imaging
CAP3	20120705	[63]	Biology, sequence assembly
CASAVA	1.8.2	[64]	Biology, NGS
CD-HIT	4.6, 4.6.4	[65]	Biology, Genomics
CDO	1.6.1	[66]	Climate
CEAS	1.0.2	[67]	Biology, Genomics
CellProfiler	2.0	[68]	Biology, Image Analysis
CGATools	1.6.0.42	[69]	Biology, NGS
Charmm	36a3	[70]	Simulation, Chemistry
Chartdirector	5.1.0	[71]	Graphics
CheckM	1.0.4	[72]	Biology, Genomics
Chimera	1.7	[73]	Biology, Modeling
ChromEvol	2.0	[74]	Biology, Phylogenetics
CIMS	4.1.2	[75]	Biology, Genomics
Circos	0.63-pre11	[76]	Biology, Visualization
CisGenome	2.0	[77]	Biology, Genomics, Peak Calling
Clann	3.2.3	[78]	Biology, Phylogenetics
CLHEP	2.2.0.1	[79]	High Energy Physics
ClonalFrame	1.1, 1.2	[80]	Biology, Genomics, NGS
ClonalFrameML	1.25	[81]	Biology, Genomics, NGS
ClustalW	2.1	[82]	Biology, Genomics
Cluster3	1.52	[83]	Biology, Genomics
Clview	20130402	[84]	Biology, Genomics
ClustalO	1.2.0	[85]	Biology, Genomics
CMake	2.8.8, 2.9.12.1, 3.1.0	[86]	Programming, Build System
CNVSeq	20110715	[87]	Biology, NGS
Cobrapy	0.3.2	[88]	Biology, Metabolomics, Modeling
Coevol	1.3c, 1.4b	[89]	Biology, Phylogenetics
CoMap	1.4.1	[90]	Biology, Genomics
CONCOCT	0.3.1	[91]	Biology, Genomics
CoNIFER	0.2.2	[92]	Biology, Genomics
Consed	23.0	[93]	Biology, Genomics
Coreutils	8.23	[94]	GNU Utilities, Computer Science
covNMR	2014	[95]	Biochemistry
CPLEX	12.6.5	[96]	Optimizer
CUDA	4.2, 5.5	[97]	Programming, Graphics
Crux	1.40	[98]	Biology, Mass-Spectrometry
Cufflinks	1.3.0, 2.0.2, 2.2.1	[99]	Biology, NGS
Cutadapt	1.1, 1.7.1, 1.8.1	[100]	Biology, NGS
DAKOTA	5.4.0	[101]	Computational Science
DaPars	0.9.0	[102]	Biology, NGS, RNA-Seq
DCMTK	3.6.0	[103]	Biology, Neuroscience, Imaging
DSSAT	4.5	[104]	Biology
DDSCAT	7.3.0	[105]	Astrophysics
DDT	4.1.0, 4.2.1	[106]	Software
Delft3D	3621	[107]	Hydrodynamics, Physics
Desmond	3.0.3.1	[108]	Simulation, Biology, Chemistry
DETONATE	1.9	[109]	Biology, NGS
Dalton	2011	[110]	Quantum Chemistry
Diamond	0.5.1	[111]	Computational Biology, Genomics
Dibig Tools	1.0	[112]	Bioinformatics, PBS, Torque, Jobs
DiffReps	1.55.4	[113]	Biology, NGS, ChIP-Seq
Dindel	1.01	[114]	Biology, NGS
DISCOVARdenovo	52488	[115]	Biology, NGS
DIYABC	1.0.4.43b, 2.0.3	[116]	Biology, Genomics
Dlpoly	4.03.4	[117]	Simulation, Biology, Chemistry
Dlpoly-Classic	1.9	[118]	Simulation, Biology, Chemistry
DNA Clust	3.0	[119]	Biology, Genomics
Dock	6.5, 6.6, 6.7	[120]	Chemistry, ligand binding prediction
DOT	2.0	[121]	Biology, Bioinformatics, Docking
Doxygen	1.8.3.1	[122]	Programming, Documentation
DSSP	2.2.1	[123]	Biology, Molecular Dynamics
DTI-TK	2.3.1	[124]	Biology, Neurology, Imaging
EA-Utils	1.1.2.537	[125]	Biology, NGS
ECTools	20140311, 20141201	[126]	Biology, Sequencing, Bioinformatics
EEGLAB	12.0.2.1b, 13.2.2b, 13.4.4b	[127]	Biology, Matlab
EIGENSOFT	4.2, 5.0.1, 6.0.1	[128]	Biology, Population
emboss	6.5.7	[129]	Biology, multi-tool suite
EMAN2	2.11	[130]	Biology
EMIRGE	20130727	[131]	Biology, NGS
Ensembl_Tools	80	[132]	Biology, Bioinformatics
EPACTS	3.2.6	[133]	Biology, Bioinformatics, Genomics
eQTLA	1.1	[134]	Biology, Genomics
Eqtlbma	1.2.2	[135]	Biology, Genotyping
Esmf	6.3.0rp1	[136]	Climate
Espresso	5.0.1, 5.2.0, 5.2.1	[137]	Modeling, Physics
ESPRIT	201211	[138]	Biology, NGS, Metagenomics
ETE2	2.1	[139]	Biology, Phylogenetics
Eval	2.2.8	[140]	Biology, Genomics, GUI
ExaBayes	1.2.1	[141]	Biology, Phylogenetics
ExaML	1.0.5, 1.0.12, 3.0.14	[142]	Biology, Phylogenetics
ExomeCNV	1.4	[143]	Biology, NGS, Genomics
Exonerate	2.2.0	[144]	Biology, Genomics
eXpress	1.3.1	[145]	Biology, NGS
FAR	2.15	[146]	Biology, Genomics
FASTA	34.26.5, 36.3.6d	[147]	Biology, Genomics
FastML	3.0	[148]	Biology, Phylogenetics, ML
FastQC	0.9.6, 0.10.1	[149]	Biology, NGS
Fastq-tools	0.7, 0.8	[150]	Biology, NGS
FastTree	2.1.7	[151]	Biology, Phylogenetics
Fastx_toolkit	0.0.13.2	[152]	Biology, NGS
Fathmm	20150225	[153]	Biology, Genomics
fcGENE	1.0.7	[154]	Biology, Genomics, SNP
Ferret	6.82	[155]	Oceanography, Meteorology
FFmpeg	2.1.3	[156]	Multimedia, audio, video
FFTW	3.3.2, 3.3.3	[157]	Math, Library, C++
FLASH	1.2.10, 1.2.11	[158]	Biology, Genomics, NGS
Flexbar	2.3	[159]	Biology, Genomics, NGS
Fluent	14.5.7, 15.0.7, 16.0	[160]	Simulation, Fluid Dynamics
FragGeneScan	1.16	[161]	Biology, NGS, Genomics
FreeBayes	0.9.6, 0.9.15, 0.9.21	[162]	Biology, NGS, SNP Calling
Freesurfer	5.2.0	[163]	Biology, Neurology, Imaging
FSL	5.0.2.2	[164]	Biology, Neurology, Imaging
Galaxy	latest	[165]	Biology, Chemistry, Other
GapFiller	1.11	[166]	Biology, NGS
Garli	2.0, 2.01	[167]	Biology, Phylogenetics
GAML	20150610	[168]	Biology, NGS
GARM	0.7.4	[169]	Biology, NGS
GASVPro	201310	[170]	Biology, NGS, Genomics
GATE	7.0	[171]	Data Analysis
GATK	1.6.9, 3.1.1, 3.3.0, 3.4.46	[172]	Biology, NGS
Gaussian	G03, G09-A.02, G09-C.01	[173]	Modeling, Computational Chemistry
Gblocks	0.91b	[174]	Genomics, Alignment tool
GCTA	1.24.7	[175]	Biology, Genomics, SNP
GDAL	1.11.2	[176]	Geospatial Data Modeling, Geospatial Library
Geant4	4.10	[177]	Physics
GEM	20130406	[178]	Biology, NGS
GEMINI	4.6.6a, 0.13.1	[179]	Biology, Genomics, Genetics
GenBank Tools	20140130	[180]	BIology< Genomics
GeneMark	2012.04	[181]	Biology, Genomics, Metagenomics
GeneSeqer	20140226	[182]	Biology, Genomics
Genewise	2.2.0	[183]	Biology, Genomics, Annotation
Genome STRiP	2.00.1602	[184]	Biology, genomics, NGS
GenomicTools	2.7.0	[185]	Biology, NGS
GenomeTools	1.5.7	[186]	Biology, Bioinformatics
GenSel	4.90	[187]	Biology, Genetics
GET_HOMOLOGUES	20150529	[188]	Biology, Genomics
GKNO	1.30.18	[189]	Biology, NGS,
Git	1.8.2.1, 1.9.0	[190]	Development, Revision Control
Globus	2.1.3	[191]	Data Transfer
GLPK	4.55	[192]	Biology, Genomics
Gmap	20150612, 20150723	[193]	Biology, Genomics
GNU	4.4.6, 4.7.2	[194]	Compilers, Programming
GnuPlot	4.6.0	[195]	Graphics, Plotting, Programming
Grace	5.1.22	[196]	Graphics, plotting, 2D
GrADS	2.0.1	[197]	Earth Science
GramCluster	1.3	[198]	Biology, Sequencing
GraphViz	2.38.0	[199]	Graphics, plotting, visualization
Gromacs	4.5.5, 4.6.5	[200]	Chemistry, Modeling, Simulation
GSNP	1.0	[201]	Biology, Bioinformatics, NGS
GSL	1.15	[202]	Library, Math, C++, C
Gsutil	4.15	[203]	Cloud, Storage, Google
Gubbins	20150519	[204]	Biology, Phylogenetics, Genomics
GULP	4.0	[205]	Material Science
HaMStR	13.2.2, 13.2.3, 13.2.4	[206]	Biology, Genomics
HapCompass	0.7.7	[207]	Biology, NGS, Genomics
Hapsembler	2.21	[208]	Biology, Genomics, NGS
HapTree	1.0	[209]	Biology, Genomics, NGS
HDF4	4.2.11	[210]	Library, Data
HDF5	1.8.9, 1.8.12, 1.8.15	[211]	Library, Data
HMMER3	3.0, 3.1b1, 3.1b2	[212]	Biology, Genomics
HMMSplicer	0.9.5	[213]	Biology, Genomics
HOMER	4.2	[214]	Biology, Genomics
HTMLDoc	1.2.82	[215]	Documentation, PDF, HTML
HTSeq	0.5.3p3, 0.6.1p1	[216]	Biology, NGS
Hyb	20141126	[217]	Biology, NGS, RNA-Seq
HyPhy	2.1.2.28	[218]	Biology, Phylogenetics
Hypre	1.10.0b, 2.8.0b	[219]	Library, Math, Physics
IBDNe	20150815	[220]	Biology, NGS
IDBA-UD	1.0.9, 1.1.0, 1.1.1	[221]	Biology, NGS
IEP	3.6	[222]	Programming, Python, Editor
IGB	8.4.1	[223]	Biology, Genomics, NGS
iGTP	1.1	[224]	Biology, Bioinformatics, Phylogenetics
illumiprocessor	20150803	[225]	Biology, Sequencing
IM and IMa	20091217	[226]	Biology, Population
IMa2	20120827	[227]	Biology, Population
ImageJ	1.48	[228]	Image manipulation
ImageMagick	6.8.8-9	[229]	Image manipulation
Intel Compilers	11.1, 2012	[230]	Programming, Compilers
IOAPI	3.1	[231]	Meteorology
Iprscan	4.8	[232]	Biology, Genomics
IQ-TREE	1.3.4, 1.3.9	[233]	Biology, Phylogenetics
ITK	4.3.1	[234]	Biology, Genomics
ITK-SNAP	3.0.0	[235]	Biology, Neuroscience, Imaging
JAGS	3.3.0	[236]	Statistics
Java	1.6.0_31, 1.7.0_02, 1.8.0_31	[237]	Java Development Kit
Jellyfish	2.1.1	[238]	Biology, NGS
JModelTest	2.1.1	[239]	Biology, Phylogenetics, Genomics
Julia	0.3.11	[240]	Programming, Languages
KaKs	1.2	[241]	Biology, Phylogenetics
Kent	20120524	[242]	Biology, NGS
Khmer	1.1, 2.0	[243]	Biology, NGS
KING	1.4	[244]	Biology, Genomics
Kallisto	0.42.3	[245]	Biology, NGS, RNA-Seq
Kmer	1934	[246]	Biology, NGS
KmerGenie	1.6741	[247]	Biology, NGS, Utilities
Kraken	0.10.4b	[248]	Biology, Genomics, Phylogenetics
LAMMPS	28Oct12, 30Sep13, 28Jun14,15May15	[249]	Molecular Dynamics Simulation
LAMP	2.5	[250]	Biology, Genomics
Last	193, 247	[251]	Biology, Sequence alignment
Lastz	1.03.02, 1.02.00	[252]	Biology, NGS
LDhat	2.2a	[253]	Biology, Genomics
LIBSVM	3.12	[254]	Machine Learning
LSC	0.3, 0.3.1	[255]	Biology, NGS, Error correction
Loci	3.3	[256]	Fluid Dynamics
LS-DYNA	700, 711, 800	[257]	Physics
Lumpy	0.2.1	[258]	Biology, SNP
LZO	2.09	[259]	Library, Data Compression
MACH	1.0.18	[260]	Biology, Genomics
Mach2VCF	20150515	[261]	Biology
M5tools	20121126	[262]	Biology, Bioinformatics, Genomics
MACS	1.4.2	[263]	Biology, ChIP-Seq
mafft	6.903, 7.215, 7.245	[264]	Biology, Multiple sequence alignment
Maker	2.10, 2.25b	[265]	Biology, Annotation, Genomics
MapSplice	2.1.7	[266]	Biology, NGS, RNA-Seq
MAPminer	1.1	[267]	Biology, Phylogenetics
MassMine	0.9.5, 0.10.0	[268]	Data Mining
Maq	0.7.1	[269]	Biology, NGS
MARK	2.0.1	[270]	Statistics
MarkerMiner	20150429, 20150511	[271]	Biology, Genomics
MaSuRCA	2.3.2	[272]	Biology, NGS
Matlab	2012a, 2013a, 2014a	[273]	Math, Simulation, Programming
MATS	2.1.0, 3.0.8, 3.0.9	[274]	BIology, NGS
Mauve	2.3.1	[275]	Biology, NGS
MCarts	1.0.2	[276]	Biology, Genomics, Markov models
MCNP	5, 6b2	[277]	Physics
MCNPX	2.7.0, 2.7.0-i8	[278]	Physics
MEGAN	5.10.3	[279]	Biology, NGS
Megraft	1.0.2	[280]	Biology, Sequencing
Melting	4.3.1	[281]	Biology, Genome, RNA, Folding
Meme	4.8.1	[282]	Biology, Motifs, Sequence analysis
Meraculous	2.0.5	[283]	Biology, NGS
Mercurial	2.7	[284]	Development, Revision Control
Merlin	1.1.2	[285]	Biogolgy, SNP
Metabin	1.0	[286]	Biology, Metagenomics
MetaCluster	5.0b	[287]	Biology, Metagenomics
MetaCV	2.3.0	[288]	Biology, NGS
METAL	20110325	[289]	Biology, Genomics
MetAMOS	1.5.0rc4-20140827	[290]	Biology, Bioinformatics, Genomics, Assembly
Metassembler	1.5	[291]	Biology, Genomics
MetaVelvet	1.2.01	[292]	Biology, NGS
Metaxa2	2.0.2	[293]	Biology, NGS
MetaGeneMark	2012.04	[294]	Biology, Genomics
Mfold	3.6	[295]	Biology, Genomics
MIA	20130301	[296]	Biology, NGS
Midnight Commander	4.6.1	[297]	Tools, Utilities
Migrate-n	3.3.0, 3.6.6	[298]	Biology, Population
Minimac	1-20130717, 2-20140915, 3-20150727	[299]	Biology, Genomics
mira	3.9.18, 4.0.rc1, 4.0.2	[300]	Biology, NGS
MISO	0.4.9, 0.5.2, 0.5.3	[301]	Biology, NGS
MMSEQ	1.0.8	[302]	Biology, NGS
MSMBuilder	2.5.1	[303]	Molecular Dynamics
MOABS	1.2.9	[304]	Biology, NGS, Genomics
Modeller	9.11, 9.13, 9.14	[305]	Biology, Modeling
Molden	5.0	[306]	Molecular, electronic structure
MolPro	2012.1p22	[307]	Quantum Chemistry, Ab Initio
mosaik	2.1.33, 2.2.3	[308]	Biology,NGS
Mothur	1.31.2, 1.36.1	[309]	Biology, Microbial Ecology
MOTU	1.1	[310]	Biology, Bioinformatics, Genomics
MP-EST	1.4	[311]	Biology, Phylogenetics
mpiP	3.4.1	[312]	Parallel Computing
MrBayes	3.2.1, 3.2.4, 3.2.5	[313]	Biology, Phylogenetics
MRIcron	201306	[314]	Biology, MRI, Imaging
MUMmer	3.23	[315]	Biology, Genomics
MUSCLE	3.8.31	[316]	Biology, Genomics
MuTect	1.1.4, 1.1.7	[317]	Biology, Genomics
MutSig	1.4	[318]	Biology, Genomics
MZMine	2.14.2, 2.15, 2.17	[319]	Biology, Spectroscopy
NAMD	2.9	[320]	Simulation, Chemistry, Biology
Nanocorrect	20150727	[321]	Biology, NGS
Nanopolish	20150904	[322]	Biology
Nbody	6	[323]	Astronomy
NCBI C++ Toolkit	12.0.0	[324]	Biology, C++, Development
NCL	6.1.2	[325]	Atmosphere Science
NCO	4.2.1, 4.4.3	[326]	Data exchange tools
Ncview	2.1.2	[327]	Data visualization
NetCDF	3.4.2, 4.2, 4.3	[328]	Data exchange, Tools
Newbler	2.7, 2.8, 2.9	[329]	Biology, NGS
Newick utils	1.6	[330]	Biology, Phylogenetics
Nextallele	20140718	[331]	Biology, Genomics
Nexus NCL	2.1.18	[332]	Biology, Phylogenetics, Library
ngsCAT	0.1	[333]	Biology, Bioinformatics, NGS
ngsTools	20150816	[334]	Biology, NGS
NGSUtils	20130722, 20150206	[335]	Biology, NGS
Nipype	0.10.0	[336]	Biology, Bioinformatics, Neuroscience, Imaging
NMRPipe	7.9	[337]	Biology, Biochemistry
Novoalign	2.08.02, 3.00.02	[338]	Biology, NGS
NWChem	6.5	[339]	Chemistry
Oases	0.2.08	[340]	Biology, NGS
Olego	1.1.2, 1.1.5, 1.1.6	[341]	Biology, NGS, RNA-Seq
OCaml	4.02.3	[342]	Programming Languages, Scripting, Development
Octave	3.6.4	[343]	Numerical Computation
Oncotator	1.5.2.0, 1.5.3.0, 1.8.0.0	[344]	Biology, Genomics
OpenBabel	2.3.2	[345]	Biology, Chemistry
OpenCL	1.1	[346]	Programming, Library
OpenCV	2.4.8	[347]	Computervision
OpenFOAM	2.1.1	[348]	Fluid Dynamics
OpenMM	6.2.0	[349]	Quantum Chemistry
OrthoFinder	0.2.5	[350]	Biology, Genomics
OrthoMCL	2.0.2, 2.0.3, 2.0.7	[351]	Biology, Genomics
p4vasp	0.3.29	[352]	Molecular, Electronic Structure
Pacbio	2.2.0, 2.3.0	[353]	Biology, Bioinformatics, NGS
Package-GFE	20150701	[354]	Biology, Genomics
PALES	122	[355]	Physics
PAML	4.7, 4.8a	[356]	Biology, Phylogenetics
Pandaseq	20140808, 20150627	[357]	Biology, Bioinformatics, NGS, Sequencing
PAPI	5.1.0.2	[358]	Software, Computing
Parallel	20150122	[359]	Programming, Languages
ParaView	4.1.0, 4.2.0, 4.3.0	[360]	Data Analysis
PartitionFinder	1.0.1, 1.1.1	[361]	Biology, Phylogenetics, Evolution
Parflow	v615	[362]	Ecology, Modeling
PASA	1.5, 2.0-r20150209	[363]	Biology, Genomics
PAUP	4.0b10	[364]	Biology, Phylogenetics
PAUDA	1.0.1	[365]	Biology, Bioinformatics, Sequence alignment
PBJelly	14.7.14, 15.2.20	[366]	Biology, Bioinformatics
pbsdrmaa	1.0.17	[367]	Libraries, Torque
PeakSplitter	1.0	[368]	Biology, Chip-Seq
PEAR	0.9.2, 0.9.6	[369]	Biology, NGS
PDT	3.18	[370]	Programming, Profiler
Perl	5.16.0	[371]	Programming, Language
PerM	0.4.0	[372]	Biology, NGS
PETSc	2.3, 3.3	[373]	Math, Numerical solvers
Phenix	1.8.1069, 1.10.2155	[374]	Crystallography
PHYLDOG	20130418	[375]	Biology, Genomics, Phylogenetics
Phyluce	c561dd9	[376]	Biology, Phylogenetics
PfamScan	1.3	[377]	Biology, Genomics
PHITS	2.52	[378]	Physics
Phonopy	1.9.2	[379]	Chemistry
PHYLIP	3.696	[380]	Biology, Phylogenetics
PhyloBayes	3.3f, 1.4f MPI	[381]	Biology, Phylogenetics
Phylosift	1.1	[382]	Biology, Genomics, Phylogenetics, Taxonomy
PhyML	3.0, 20121109	[383]	Biology, Phylogenetics
Picard	1.69, 1.72, 1.80	[384]	Biology, NGS
PICRUSt	1.0.0	[385]	Biology, Phylogenics
PLAST	1.0	[386]	Biology, Bioinformatics
Plink	1.07, 1.90b3	[387]	Biology, GWAS
PLINKSEQ	0.10	[388]	Biology, Genomics
PluMiST	1.1	[389]	Biology, Phylogenetics, Genomics
PolyPhen	2.2.2.r405b	[390]	Biology, Genomics
Poretools	0.5.0	[391]	Biology, Sequencing
POV-Ray	3.7	[392]	3D, Graphics
Preseq	0.0.4	[393]	Biology, NGS
Primer3	2.3.4	[394]	Biology, Genomics
ProfessAtQE	2014	[395]	Material Science, Molecular Dynamics
Prokka	1.10	[396]	Biology, Genomics, Bioinformatics, Assembly
ProBABEL	0.4.2, 0.4.3, 0.4.5	[397]	Biology, Genomics, GWAS
Probalign	1.4	[398]	Biology, Genomics
Proovread	1.03rcl	[399]	Biology, Genomics, NGS
Proteinortho	4.26	[400]	Biology, Genomics
PROVEAN	1.1.5	[401]	Biology, Genomics
Python	2.7.6, 3.5.0	[402]	Biology, Genomics, NGS
Pyrad	3.0.63	[403]	Biology, Sequencing Alignment, Assembly
QDD	3.1.2	[404]	Programming, scripting, language
QIIME	1.5.0	[405]	Biology, Ecology
QT	4.8.3	[406]	Computer Science
QUAST	2.3	[407]	Biology, NGS
Quantas	1.0.4, 1.0.8	[408]	Biology, Bioinformatics, NGS
QualiMap	2.1.1	[409]	Biology, Sequence alignment
Quickquartet	1.0.0	[410]	Biology, Phylogenetics
R	Rmpi/2.15.1, 3.0.2, 3.2.0	[411]	Statistics, Programming
R8S	1.71, 1.8	[412]	Biology, Evolution
RADICAL	0.2	[413]	Biology, Phylogenetics, Genomics
REAPR	1.0.18	[414]	Biology, Bioinformatics, Assembly
RAxML	8.1.23, 8.2.2, 8.2.3	[415]	Biology, Phylogenetics
RepeatExplorer	20150506	[416]	Biology, Genomics
RepeatMasker	3.3.0	[417]	Biology, Genomics
Reptile	1.1	[418]	Biology, NGS, error correction
riboPicker	0.4.3	[419]	Biology, Sequence
RNAhybrid	2.1.1	[420]	Biology, Genomics
ROOT	6.0	[421]	Data Analysis
Roary	3.4.1	[422]	Biology, Genomics
Rosetta	2014wk4	[423]	Biology, Structure, Modelling
RSEG	0.4.8	[424]	Biology, NGS
RSEM	1.1.17, 1.2.7, 1.2.19	[425]	Biology, NGS, RNA-Seq
RSeQC	2.3.7, 2.6.2	[426]	Biology, NGS, RNA-Seq
Ruby	1.9.3-p0	[427]	Programming, Scripting, Language
Sailfish	0.6.3	[428]	Biology, NGS, RNA-Seq
Sambamba	0.5.0-dev, 0.5.1	[429]	Biology, NGS
Samstat	1.08	[430]	Biology, NGS, Bioinformatics, Sequencing
Samblaster	0.1.14	[431]	Biology, NGS
samtools	1.0, 1.1, 1.2	[432]	Biology, NGS
SAS	9.3	[433]	Statistics, Graphing
SATe	2.2.7	[434]	Biology, Phylogenetics
Scala	2.11.5	[435]	Programming, Language
Scalablast	2.4.53	[436]	Biology, Genomics
Scalpel	0.1.1	[437]	Biology, NGS
SHAPEIT	2.5.5	[438]	Biology, SNP
Sharcgs	1.2.11	[439]	Biology, NGS, Assembly
Schrodinger	2012, 2013	[440]	Simulation, chemistry
SCons	2.3.0	[441]	Programming
SCRATCH1D	1.0	[442]	Biology, Genomics
Scythe	0.991	[443]	Biology, NGS
Segemehl	0.1.9	[444]	Biology, NGS, Mapper
SEPP	1.0, 3.0	[445]	Biology, Phylogenetics, HMM
Seq-Gen	1.3.3	[446]	Biology, Phylogenetics
SeqPrep	0.5	[447]	Biology, NGS
SeqMap	1.0.13	[448]	Biology, NGS
Seqtk	20140729	[449]	Biology, NGS
SEQuel	1.0.1	[450]	Biology, NGS
SeqyClean	1.8.10	[451]	Biology, NGS, Bioinformatics
ShoRAH	20131204	[452]	Biology, NGS, quality filter
SHRiMP	2.2.3	[453]	Biology, NGS
Sickle	1.200, 1.33	[454]	Biology, NGS, quality filter
Siesta	2.0.2,3.1	[455]	Simulation, Physics, Ab Initio
SIFT	4.0.3b	[456]	Biology, Genomics
Silo	4.7	[457]	Library, Data
SIPeS	2.0	[458]	Biology, Bioinformatics, ChIP-Seq
Slicer	4.3.1	[459]	Biology, Imaging
SMALT	0.7.6	[460]	Biology, NGS
Snap	20100728	[461]	Biology, Genomics
SNAPE-pooled	20130407	[462]	Biology, SNP
SNeP	1.1	[463]	Biology, Phylogenics
SnpEff	3.3h, 4.0e, 4.1i	[464]	Biology, NGS, Genomics
SNPhylo	20140701	[465]	Bilogy, Phylogenetics
SOAPdenovo	1.05	[466]	Biology, NGS
SOAPdenovo-Trans	1.01, 1.03	[467]	Biology, NGS
SOAPsplice	1.10	[468]	Biology, NGS
SparCC	201402	[469]	Microbial Ecology
Spades	3.1.0, 3.5.0, 3.6.0	[470]	Biology, NGS
Spanki	0.4.1, 0.4.3, 0.5.0	[471]	Biology, NGS, RNA-Seq
SPARTA+	2.60	[472]	Chemistry
Spidey	20150922	[473]	Biology, Genomics
SPIMAP	1.1	[474]	Biology, Phylogenetics
SpliceTrap	0.90.5	[475]	Biology, NGS, RNA-Seq
SPM	8	[476]	Biology, Statistics, Neurology, Imaging
Sputnik	1.0	[477]	Biology, Genomics
SQLite	3.8.8.2	[478]	Database
SQL_Developer	4.1.2	[479]	Programming, Oracle, Sql
SRA	2.1.10	[480]	biology, NGS
SSPACE	2.0, 3.0	[481]	Biology, NGS
Stacks	0.9995	[482]	Biology, Genomics, NGS
STAR	2.3.0e	[483]	Biology, NGS, Alignment
STAR-CCM+	8.06	[484]	Mechanical Engineering
Stata	10.1, 13	[485]	Statistics, Data analysis
Stringtie	0.97	[486]	Biology, NGS, Alignment
Structure	2.3.3, 2.3.4	[487]	Biology, Population
SUNDIALS	2.3.0, 2.5.0	[488]	Numerical Solver
SVDetect	0.8b	[489]	Biology, NGS, SNP
swak4Foam	2.x	[490]	Fluid Dynamics
swarm	1.2.11	[491]	Data Analysis
Swig	2.0.9	[492]	Programming, C, C++, Python
SwitchSeq	20140907	[493]	Biology, NGS
Syzygy	1.2.7	[494]	Biology, Genomics
TASSEL	5.0	[495]	Biology, Genomics
TAU	2.21.4, 2.23	[496]	Profiling, Tracing, Programming
T-Coffee	9.03.r1318	[497]	Biology, Genomics, Multiple Alignment
TESS	2.3.1	[498]	Biology, Genomics, Markov
tgicl	2.1	[499]	Biology, sequencing, clustering
Tmux	2.0	[500]	GNU, Terminal Multiplexer
TomoPy	0.0.3	[501]	Biology, Neuroimaging
Tophat	1.4.1, 2.0.13, 2.1.0	[502]	Biology, NGS
Totalview	8.12.0	[503]	Computer Science
TPP	4.7.0	[504]	Bioinformatics, MassSpec
TrackTools	2011	[505]	Bioinformatics
TrackVis	0.5.2.2	[506]	Biology, Spectroscopy
Tracula	5.3.2014_05_26	[507]	Biology, Bioinformatics, Neuroscience, Imaging
TraitRate	1.1	[508]	Biology, Evolution
TransDecoder	20140704, 2.0.1	[509]	Biology, NGS
Transrate	1.0.1	[510]	Biology, Assembly
TreeFix	1.1.7, 1.1.10	[511]	Biology, Phylogenetics
TreePL	20150305	[512]	Biology, Phylogenetics
TRF	4.04	[513]	Biology, Genomics
Trilinos	11.4.1, 11.8.1	[514]	Math Algorithm
trimAl	1.2	[515]	Biology, Genomics, Sequence Alignment
Trim Galore	0.2.8	[516]	Biology, NGS
Trimmomatic	0.22, 0.32	[517]	Biology, NGS
Trinity	r20150215-2.0.4, r20150302-2.0.6	[518]	Biology, NGS, RNA-Seq
Trinotate	2.0.1	[519]	Biology
TRNAscan-SE	1.23	[520]	Biology, NGS, Bioinformatics
Twinscan	4.1.2	[521]	Biology, Genomics
usearch	7.0.1001-64, 8.0.1517	[522]	Biology, Sequence analysis
UDUNITS	2.2.17	[523]	Library, Units, Programming
UNAFold	3.8	[524]	Biology, Genome, RNA, Folding
UProC	1.2.0	[525]	Biology, Genomics
Valgrind	3.9.0	[526]	Computer Science
VarScan	2.3.6	[527]	Biology, NGS, Genomics
VASP	5.3.2, 5.3.3, 5.3.5	[528]	Quantum Chemistry, Ab Initio
VAST-TOOLS	20150506	[529]	Biology, NGS, RNA-Seq
VCFLib	20141119, 20150313	[530]	Biology, NGS, Genomics
VCFtools	0.1.12a, 0.1.12b, 0.1.14	[531]	Biology, SNPs
velvet	1.2.06, 1.2.07, 1.2.10	[532]	Biology, Genomics, NGS
VEP	74	[533]	Biology, NGS
VICUNA	1.3	[534]	Biology, Assembly
Vim	7.4.5	[535]	Programming, Scripting, Language
vmd	1.9.1	[536]	Biology, Visualization
VSearch	20151022	[537]	Biology, NGS
VTK	6.1.0	[538]	Visualization, Graphics
Wannier90	1.2, 2.0.0	[539]	Computational Physics
WebLogo	3.3	[540]	Biology, Genomics
WDSSII	1	[541]	Meteorology
WIEN2k	12.1	[542]	Material Science, Chemistry
Wgs or Celera	8.2, 8.3rc1, 8.3rc1.r4638	[543]	Biology, NGS
wublast	2.0	[544]	Biology, Sequence Alignment
YAHA	0.1.82	[545]	Biology NGS
XCrySDen	1.5.60	[546]	Computational Material Science
Yambo	3.3.0	[547]	Physics
YASM	1.3.0	[548]	Computer Science
Yasra	2.32	[549]	Biology, NGS

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