Installed Software

Installed Software List

Last updated 2015-01-29.

Note: Click on the icons to the right of the column headings to sort the table.

0-9 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 Z

Name	Version	Website	Category
AbInit	6.12.3	[1]	Ab Initio Quantum Chemistry, Density Functional Theory
Abyss	1.3.4, 1.3.7	[2]	Biology, NGS
AFNI	2011_12_21_1014	[3]	Biology, Statistics, Imaging, Neurology
Agalma	0.2.1, 0.3.5	[4]	Biology, Bioinformatics, Genomics, SNP
ALLPATHS-LG	42316, 44837	[5]	Biology, NGS
Amber	11, 12, 14	[6]	Simulation, chemistry
AMOS	3.1.0	[7]	Biology, Genomics, NGS
ANNOVAR	20120621,20121023,20130321	[8]	Biology, Genomics
Atlas	3.10.1, 3.11.17	[9]	Library, Math
Amuse	6.0	[10]	Astrophysics
Affymetrix Power Tools	1.15.0	[11]	Biology, Genomics, Microarray
ARC	20140312	[12]	Biology, NGS
Astral	4.4.4	[13]	Biology, Bioinformatics, NGS, Phylogenetics
AtomEye	3	[14]	Material Science
ATRAM	20140624	[15]	Biology, NGS
Augustus	2.6	[16]	Biology, NGS
BamBam	1.0	[17]	Biology, NGS
Bamstats	20140602	[18]	Biology, NGS
Bamtools	2.1.1	[19]	Biology, NGS
BamUtil	1.0.2	[20]	Biology, NGS
BayesRate	1.3.43	[21]	Biology, Phylogenetics
Bbcp	12.08.17.00.0	[22]	Network file transfer
Bcftools	20140618	[23]	Biology, Genomics, NGS
BEAGLE	3.2.2	[24]	Biology, Genetics, Genotyping
BEAST	1.7.5, 1.8.1, 2.1.3	[25]	Biology, Phylogenetics
Bedops	2.4.2	[26]	Biology, Bioinformatics, Sequence, NGS
BEDTools	2.16.2, 2.17.0	[27]	Biology, NGS
BEST	2.3	[28]	Biology, Phylogenetics
BETA	1.0.5	[29]	Biology, NGS
BFAST	0.7.0	[30]	Biology, NGS
Bismark	0.7.4, 0.7.7, 0.13.0	[31]	Biology, NGS, Methylation
Bioconductor	Latest	[32]	Biology, R, Statistics
BioPerl	1.006901	[33]	Biology, Perl
PHYLDOG	20130418	[34]	Biology, Genomics, Phylogenetics
Phyluce	c561dd9	[35]	Biology, Phylogenetics
BioPython	1.59	[36]	Biology, Python
BLASR	20130815	[37]	Biology, NGS
NCBI BLAST	2.2.27, 2.2.28, 2.2.29	[38]	Biology, Sequence alignment
Blast2go	2.5.0-20120705	[39]	Biology, Annotation
BLAT	20120524	[40]	Biology, Sequence alignment
Blender	2.63	[41]	Graphics
Boost	1.49.0, 1.53.0, 1.54.0	[42]	C++, Library
Bowtie	0.12.9, 1.0.0	[43]	Biology, NGS
Bowtie2	2.1.0, 2.2.2, 2.2.3, 2.2.4	[44]	Biology, NGS
BPP	2.2, 1.9.0	[45]	Biology, Phylogenetics
BRANCH	1.8.1	[46]	Biology, NGS, Mapping
Bsmap	2.74, 2.87	[47]	Biology, NGS, Methylation
Bwa	0.6.1, 0.7.9a, 0.7.10	[48]	Biology, NGS
Camino	20140723	[49]	Biology, Neuroscience, Imaging
CAP3	20120705	[50]	Biology, sequence assembly
CASAVA	1.8.2	[51]	Biology, NGS
CD-HIT	4.6	[52]	Biology, Genomics
CDO	1.6.1	[53]	Climate
CEAS	1.0.2	[54]	Biology, Genomics
CellProfiler	2.0	[55]	Biology, Image Analysis
CGATools	1.6.0.42	[56]	Biology, NGS
Charmm	36a3	[57]	Simulation, Chemistry
Chartdirector	5.1.0	[58]	Graphics
Chimera	1.7	[59]	Biology, Modeling
ChromEvol	2.0	[60]	Biology, Phylogenetics
CIMS	4.1.2	[61]	Biology, Genomics
Circos	0.63-pre11	[62]	Biology, Visualization
CisGenome	2.0	[63]	Biology, Genomics, Peak Calling
Clann	3.2.3	[64]	Biology, Phylogenetics
CLHEP	2.2.0.1	[65]	High Energy Physics
ClonalFrame	1.1, 1.2	[66]	Biology, Genomics, NGS
ClustalW	2.1	[67]	Biology, Genomics
Cluster3	1.52	[68]]	Biology, Genomics
Clview	20130402	[69]	Biology, Genomics
CMake	2.8.8, 2.9.12.1, 3.1.0	[70]	Programming, Build System
CNVSeq	20110715	[71]	Biology, NGS
Coevol	1.3c, 1.4b	[72]	Biology, Phylogenetics
CoMap	1.4.1	[73]	Biology, Genomics
CONCOCT	0.3.1	[74]	Biology, Genomics
Consed	23.0	[75]	Biology, Genomics
Coreutils	8.23	[76]	GNU Utilities, Computer Science
covNMR	2014	[77]	Biochemistry
CUDA	4.2, 5.5	[78]	Programming, Graphics
Crux	1.40	[79]	Biology, Mass-Spectrometry
Cufflinks	1.3.0, 2.0.2, 2.2.1	[80]	Biology, NGS
Cutadapt	1.1	[81]	Biology, NGS
DAKOTA	5.4.0	[82]	Computational Science
DaPars	0.9.0	[83]	Biology, NGS, RNA-Seq
DCMTK	3.6.0	[84]	Biology, Neuroscience, Imaging
DSSAT	4.5	[85]	Biology
DDSCAT	7.3.0	[86]	Astrophysics
DDT	4.1.0, 4.2.1	[87]	Software
Delft3D	3621	[88]	Hydrodynamics, Physics
Desmond	3.0.3.1	[89]	Simulation, Biology, Chemistry
Dalton	2011	[90]	Quantum Chemistry
Diamond	0.5.1	[91]	Computational Biology, Genomics
Dibig Tools	1.0	[92]	Bioinformatics, PBS, Torque, Jobs
DiffReps	1.55.4	[93]	Biology, NGS, ChIP-Seq
Dindel	1.01	[94]	Biology, NGS
DIYABC	1.0.4.43b, 2.0.3	[95]	Biology, Genomics
Dlpoly	4.03.4	[96]	Simulation, Biology, Chemistry
DNA Clust	3.0	[97]	Biology, Genomics
Dock	6.5, 6.6	[98]	Chemistry, ligand binding prediction
DOT	2.0	[99]	Biology, Bioinformatics, Docking
Doxygen	1.8.3.1	[100]	Programming, Documentation
DSSP	2.2.1	[101]	Biology, Molecular Dynamics
DTI-TK	2.3.1	[102]	Biology, Neurology, Imaging
E EA-Utils	1.1.2.537	[103]	Biology, NGS
ECTools	20140311, 20141201	[104]	Biology, Sequencing, Bioinformatics
EEGLAB	12.0.2.1b	[105]	Biology, Matlab
EIGENSOFT	4.2, 5.0.1	[106]	Biology, Population
emboss	6.5.7	[107]	Biology, multi-tool suite
EMIRGE	20130727	[108]	Biology, NGS
eQTLA	1.1	[109]	Biology, Genomics
Eqtlbma	1.2.2	[110]	Biology, Genotyping
Espresso	5.0.1	[111]	Modeling, Physics
ESPRIT	201211	[112]	Biology, NGS, Metagenomics
ETE2	2.1	[113]	Biology, Phylogenetics
Eval	2.2.8	[114]	Biology, Genomics, GUI
ExaBayes	1.2.1	[115]	Biology, Phylogenetics
ExaML	1.0.3, 1.0.5, 1.0.12	[116]	Biology, Phylogenetics
ExomeCNV	1.4	[117]	Biology, NGS, Genomics
Exonerate	2.2.0	[118]	Biology, Genomics
eXpress	1.3.1	[119]	Biology, NGS
FAR	2.15	[120]	Biology, Genomics
FASTA	34.26.5, 36.3.6d	[121]	Biology, Genomics
FastML	3.0	[122]	Biology, Phylogenetics, ML
FastQC	0.9.6, 0.10.1	[123]	Biology, NGS
FastTree	2.1.7	[124]	Biology, Phylogenetics
Fastx_toolkit	0.0.13.2	[125]	Biology, NGS
fcGENE	1.0.7	[126]	Biology, Genomics, SNP
Ferret	6.82	[127]	Oceanography, Meteorology
FFmpeg	2.1.3	[128]	Multimedia, audio, video
FFTW	3.3.2, 3.3.3	[129]	Math, Library, C++
FLASH	1.2.10	[130]	Biology, Genomics, NGS
Flexbar	2.3	[131]	Biology, Genomics, NGS
Fluent	14.5.7, 15.0	[132]	Simulation, Fluid Dynamics
FragGeneScan	1.16	[133]	Biology, NGS, Genomics
FreeBayes	0.9.6, 0.9.15	[134]	Biology, NGS, SNP Calling
Freesurfer	5.2.0	[135]	Biology, Neurology, Imaging
FSL	5.0.2.2	[136]	Biology, Neurology, Imaging
G GapFiller	1.11	[137]	Biology, NGS
Garli	2.0, 2.01	[138]	Biology, Phylogenetics
GASVPro	201310	[139]	Biology, NGS, Genomics
GATE	7.0	[140]	Data Analysis
GATK	1.6.9, 2.7.4, 3.1.1	[141]	Biology, NGS
Gaussian	E01, G03, G09-A.02, G09-C.01	[142]	Modeling, Computational Chemistry
Geant4	4.10	[143]	Physics
GEM	20130406	[144]	Biology, NGS
GEMINI	4.6.6a	[145]	Biology, Genomics, Genetics
GenBank Tools	20140130	[146]	BIology< Genomics
GeneMark	2012.04	[147]	Biology, Genomics, Metagenomics
Genewise	2.2.0	[148]	Biology, Genomics, Annotation
GenomicTools	2.7.0	[149]	Biology, NGS
GKNO	1.30.18	[150]	Biology, NGS
Git	1.8.2.1	[151]	Development, Revision Control
Globus	2.1.3	[152]	Data Transfer
GLPK	4.55	[153]	Biology, Genomics
Gmap	20130618, 20130720, 20140530	[154]	Biology, Genomics
GNU	4.4.6, 4.7.2	[155]	Compilers, Programming
GnuPlot	4.6.0	[156]	Graphics, Plotting, Programming
Grace	5.1.22	[157]	Graphics, plotting, 2D
GrADS	2.0.1	[158]	Earth Science
GraphViz	2.38.0	[159]	Graphics, plotting, visualization
Gromacs	4.5.5, 4.6.5	[160]	Chemistry, Modeling, Simulation
GSNP	1.0	[161]	Biology, Bioinformatics, NGS
GSL	1.15	[162]	Library, Math, C++, C
GULP	4.0	[163]	Material Science
HaMStR	v8b	[164]	Biology, Genomics
HapCompass	0.7.7	[165]	Biology, NGS, Genomics
Hapsembler	2.21	[166]	Biology, Genomics, NGS
HapTree	1.0	[167]	Biology, Genomics, NGS
HDF5	1.8.9, 1.8.12	[168]	Library, Data
HMMER3	3.0, 3.1b1	[169]	Biology, Genomics
HMMSplicer	0.9.5	[170]	Biology, Genomics
HOMER	4.2	[171]	Biology, Genomics
HTMLDoc	1.2.82	[172]	Documentation, PDF, HTML
HTSeq	0.5.3p3, 0.6.1p1	[173]	Biology, NGS
HyPhy	2.1.2.28	[174]	Biology, Phylogenetics
Hypre	1.10.0b, 2.8.0b	[175]	Library, Math, Physics
IDBA-UD	1.0.9, 1.1.0	[176]	Biology, NGS
iGTP	1.1	[177]	Biology, Bioinformatics, Phylogenetics
IM and IMa	20091217	[178]	Biology, Population
IMa2	20120827	[179]	Biology, Population
ImageJ	1.48	[180]	Image manipulation
ImageMagick	6.8.8-9	[181]	Image manipulation
Intel Compilers	11.1, 2012	[182]	Programming, Compilers
IOAPI	3.1	[183]	Meteorology
Iprscan	4.8	[184]	Biology, Genomics
ITK	4.3.1	[185]	Biology, Genomics
ITK-SNAP	3.0.0	[186]	Biology, Neuroscience, Imaging
JAGS	3.3.0	[187]	Statistics
Java	1.6.0_31, 1.7.0_02	[188]	Java Development Kit
Jellyfish	2.1.1	[189]	Biology, NGS
JModelTest	2.1.1.	[190]	Biology, Phylogenetics, Genomics
KaKs	1.2	[191]	Biology, Phylogenetics
Kent	20120524	[192]	Biology, NGS
Khmer	1.1	[193]	Biology, NGS
KING	1.4	[194]	Biology, Genomics
Kmer	1934	[195]	Biology, NGS
KmerGenie	1.6741	[196]	Biology, NGS, Utilities
Kraken	0.10.4b	[197]	Biology, Genomics, Phylogenetics
LAMMPS	28Oct12, 30Sep13, 28Jun14	[198]	Molecular Dynamics Simulation
Last	193, 247	[199]	Biology, Sequence alignment
Lastz	1.03.02, 1.02.00	[200]	Biology, NGS
LIBSVM	3.12	[201]	Machine Learning
LSC	0.3, 0.3.1	[202]	Biology, NGS, Error correction
Loci	3.3	[203]	Fluid Dynamics
LS-DYNA	700, 711	[204]	Physics
Lumpy	0.2.1	[205]	Biology, SNP
MACH	1.0.18	[206]	Biology, Genomics
M5tools	20121126	[207]	Biology, Bioinformatics, Genomics
MACS	1.4.2	[208]	Biology, ChIP-Seq
mafft	7.037, 6.903	[209]	Biology, Multiple sequence alignment
Maker	2.10, 2.25b	[210]	Biology, Annotation, Genomics
MapSplice	2.1.7	[211]	Biology, NGS, RNA-Seq
Maq	0.7.1	[212]	Biology, NGS
MARK	2.0.1	[213]	Statistics
Matlab	2012a, 2013a, 2014a	[214]	Math, Simulation, Programming
MATS	2.1.0, 3.0.6b, 3.0.8	[215]	BIology, NGS
Mauve	2.3.1	[216]	Biology, NGS
MCarts	1.0.2	[217]	Biology, Genomics, Markov models
MCNP	5, 6b2	[218]	Physics
MCNPX	2.7.0, 2.7.0-i8	[219]	Physics
Melting	4.3.1	[ http://sourceforge.net/projects/melting/]	Biology, Genome, RNA, Folding
Meme	4.8.1	[220]	Biology, Motifs, Sequence analysis
Mercurial	2.7	[221]	Development, Revision Control
Metabin	1.0	[222]	Biology, Metagenomics
MetaCluster	5.0beta	[223]	Biology, Metagenomics
MetaCV	2.3.0	[224]	Biology, NGS
METAL	20110325	[225]	Biology, Genomics
MetAMOS	1.5.0rc4-20140827	[226]	Biology, Bioinformatics, Genomics, Assembly
MetaVelvet	1.2.01	[227]	Biology, NGS
MetaGeneMark	2012.04	[228]	Biology, Genomics
Mfold	3.6	[229]	Biology, Genomics
MIA	20130301	[230]	Biology, NGS
Midnight Commander	4.6.1	[231]	Tools, Utilities
Migrate-n	3.3.0	[232]	Biology, Population
mira	3.2.0, 3.4.0.1, 3.9.9, 3.9.18, 4.0.rc1	[233]	Biology, NGS
MISO	0.4.4, 0.4.9	[234]	Biology, NGS
MMSEQ	1.0.8	[235]	Biology, NGS
MSMBuilder	2.5.1	[236]	Molecular Dynamics
MOABS	1.2.9	[237]	Biology, NGS, Genomics
Modeller	9.11, 9.13, 9.14	[238]	Biology, Modeling
Molden	5.0	[239]	Molecular, electronic structure
MolPro	2012.1p22	[240]	Quantum Chemistry, Ab Initio
mosaik	2.1.33	[241]	Biology,NGS
Mothur	1.31.2	[242]	Biology, Microbial Ecology
MOTU	1.1	[243]	Biology, Bioinformatics, Genomics
MP-EST	1.4	[244]	Biology, Phylogenetics
mpiP	3.4.1	[245]	Parallel Computing
MrBayes	3.2.1	[246]	Biology, Phylogenetics
MRIcron	201306	[247]	Biology, MRI, Imaging
MUMmer	3.23	[248]	Biology, Genomics
MUSCLE	3.8.31	[249]	Biology, Genomics
MZMine	2.10	[250]	Biology, Spectroscopy
NAMD	2.9	[251]	Simulation, Chemistry, Biology
Nbody	6	[252]	Astronomy
NCBI C++ Toolkit	12.0.0	[253]	Biology, C++, Development
NCL	6.1.2	[254]	Atmosphere Science
NCO	4.2.1, 4.4.3	[255]	Data exchange tools
Ncview	2.1.2	[256]	Data visualization
NetCDF	3.4.2, 4.2, 4.3	[257]	Data exchange, Tools
Newbler	2.6, 2.7	[258]	Biology, NGS
Nextallele	20140718	[259]	Biology, Genomics
Nexus NCL	2.1.18	[260]	Biology, Phylogenetics, Library
ngsCAT	0.1	[261]	Biology, Bioinformatics, NGS
NGSUtils	20130722	[262]	Biology, NGS
Nipype	0.10.0	[263]	Biology, Bioinformatics, Neuroscience, Imaging
NMRPipe	7.9	[264]	Biology, Biochemistry
Novoalign	2.08.02, 3.00.02	[265]	Biology, NGS
Oases	0.2.08	[266]	Biology, NGS
Olego	1.1.2, 1.1.5	[267]	Biology, NGS, RNA-Seq
Octave	3.6.4	[268]	Numerical Computation
OpenBabel	2.3.2	[269]	Biology, Chemistry
OpenCL	1.1	[270]	Programming, Library
OpenCV	2.4.8	[271]	Computervision
OpenFOAM	2.1.1	[272]	Fluid Dynamics
OpenMM	6.2.0	[273]	Quantum Chemistry
OrthoMCL	2.0.2, 2.0.3, 2.0.7	[274]	Biology, Genomics
p4vasp	0.3.29	[275]	Molecular, Electronic Structure
Pacbio	2.2.0.133377	[276]	Biology, Bioinformatics, NGS
PALES	122	[277]	Physics
PAML	4.7, 4.8a	[278]	Biology, Phylogenetics
Pandaseq	20140808	[279]	Biology, Bioinformatics, NGS, Sequencing
PAPI	5.1.0.2	[280]	Software, Computing
Parallel	20150122	[281]	Programming, Languages
ParaView	4.1.0	[282]	Data Analysis
PartitionFinder	1.0.1, 1.1.1	[283]	Biology, Phylogenetics, Evolution
Parflow	v615	[284]	Ecology, Modeling
PASA	1.5, 2.0-r20130605p1, 2.0-r20130907	[285]	Biology, Genomics
PAUP	4.0b10	[286]	Biology, Phylogenetics
PBJelly	14.7.14	[287]	Biology, Bioinformatics
pbsdrmaa	1.0.17	[288]	Libraries, Torque
PeakSplitter	1.0	[289]	Biology, Chip-Seq
PEAR	0.9.2	[290]	Biology, NGS
PDT	3.18	[291]	Programming, Profiler
Perl	5.16.0	[292]	Programming, Language
PerM	0.4.0	[293]	Biology, NGS
PETSc	2.3, 3.3	[294]	Math, Numerical solvers
Phenix	1.8.1069	[295]	Crystallography
PHITS	2.52	[296]	Physics
PhyloBayes	3.3f, 1.4f MPI	[297]	Biology, Phylogenetics
Phylosift	1.1	[298]	Biology, Genomics, Phylogenetics, Taxonomy
PhyML	3.0, 20121109	[299]	Biology, Phylogenetics
Picard	1.69, 1.72, 1.80	[300]	Biology, NGS
PLAST	1.0	[301]	Biology, Bioinformatics
Plink	1.07	[302]	Biology, GWAS
PLINKSEQ	0.10	[303]	Biology, Genomics
PluMiST	1.1	[304]	Biology, Phylogenetics, Genomics
Preseq	0.0.4	[305]	Biology, NGS
Primer3	2.3.4	[306]	Biology, Genomics
Prokka	1.10	[307]	Biology, Genomics, Bioinformatics, Assembly
ProBABEL	0.4.2, 0.4.3	[308]	Biology, Genomics, GWAS
Proovread	1.03rcl	[309]	Biology, Genomics, NGS
Proteinortho	4.26	[310]	Biology, Genomics
python	2.6.8, 2.7.3, 2.7.5, 2.7.6, 2.7.8	[311]	Biology, Genomics, NGS
QDD	3.1.2	[312]	Programming, scripting, language
QIIME	1.5.0	[313]	Biology, Ecology
QT	4.8.3	[314]	Computer Science
QUAST	2.3	[315]	Biology, NGS
Quickquartet	1.0.0	[316]	Biology, Phylogenetics
R	2.15.1, 2.15.0-mpi, Rmpi/2.15.1, 3.0.0, 3.0.1, 3.0.2	[317]	Statistics, Programming
R8S	1.71	[318]	Biology, Evolution
RADICAL	0.2	[319]	Biology, Phylogenetics, Genomics
RAxML	7.9.1, 8.0.25, 8.1.12	[320]	Biology, Phylogenetics
RepeatMasker	3.3.0	[321]	Biology, Genomics
Reptile	1.1	[322]	Biology, NGS, error correction
riboPicker	0.4.3	[323]	Biology, Sequence
RNAhybrid	2.1.1	[324]	Biology, Genomics
ROOT	6.0	[325]	Data Analysis
Rosetta	2014wk4	[326]	Biology, Structure, Modelling
RSEG	0.4.8	[327]	Biology, NGS
RSEM	1.1.17, 1.2.7, 1.2.19	[328]	Biology, NGS, RNA-Seq
Ruby	1.9.3-p0	[329]	Programming, Scripting, Language
Sailfish	0.6.3	[330]	Biology, NGS, RNA-Seq
Sambamba	0.5.0-dev	[331]	Biology, NGS
Samstat	1.08	[332]	Biology, NGS, Bioinformatics, Sequencing
Samblaster	0.1.14	[333]	Biology, NGS
samtools	0.1.16, 0.1.18, 0.1.19	[334]	Biology, NGS
SAS	9.3	[335]	Statistics, Graphing
SATe	2.2.7	[336]	Biology, Phylogenetics
Scalablast	2.4.53	[337]	Biology, Genomics
Scalpel	0.1.1	[338]	Biology, NGS
Sharcgs	1.2.11	[339]	Biology, NGS, Assembly
Schrodinger	2012, 2013	[340]	Simulation, chemistry
SCons	2.3.0	[341]	Programming
Scythe	0.991	[342]	Biology, NGS
Segemehl	0.1.9	[343]	Biology, NGS, Mapper
SeqPrep	0.5	[344]	Biology, NGS
SeqMap	1.0.13	[345]	Biology, NGS
Seqtk	20140729	[346]	Biology, NGS
SEQuel	1.0.1	[347]	Biology, NGS
SeqyClean	1.8.10	[348]	Biology, NGS, Bioinformatics
ShoRAH	20131204	[349]	Biology, NGS, quality filter
SHRiMP	2.2.3	[350]	Biology, NGS
Sickle	1.200, 1.33	[351]	Biology, NGS, quality filter
Siesta	2.0.2,3.1	[352]	Simulation, Physics, Ab Initio
SIFT	4.0.3b	[353]	Biology, Genomics
Silo	4.7	[354]	Library, Data
SIPeS	2.0	[355]	Biology, Bioinformatics, ChIP-Seq
Slicer	4.3.1	[356]	Biology, Imaging
SMALT	0.7.6	[357]	Biology, NGS
Snap	20100728	[358]	Biology, Genomics
SnpEff	3.3h, 4.0e	[359]	Biology, NGS, Genomics
SOAPdenovo	1.05	[360]	Biology, NGS
SOAPdenovo-Trans	1.01, 1.03	[361]	Biology, NGS
SOAPsplice	1.10	[362]	Biology, NGS
SparCC	201402	[363]	Microbial Ecology
Spades	2.5.0, 2.5.1, 3.0.0, 3.1.0, 3.5.0	[364]	Biology, NGS
Spanki	0.4.1, 0.4.3	[365]	Biology, NGS, RNA-Seq
SPARTA+	2.60	[366]	Chemistry
SPIMAP	1.1	[367]	Biology, Phylogenetics
SpliceTrap	0.90.5	[368]	Biology, NGS, RNA-Seq
SPM	8	[369]	Biology, Statistics, Neurology, Imaging
Sputnik	1.0	[370]	Biology, Genomics
SRA	2.1.10	[371]]	biology, NGS
SSPACE	2.0	[372]	Biology, NGS
Stacks	0.9995	[373]	Biology, Genomics, NGS
STAR	2.3.0e	[374]	Biology, NGS, Alignment
STAR-CCM+	8.06	[375]	Mechanical Engineering
Stata	10.1, 13	[376]	Statistics, Data analysis
Stringtie	0.97	[377]	Biology, NGS, Alignment
Structure	2.3.3, 2.3.4	[378]	Biology, Population
SUNDIALS	2.3.0, 2.5.0	[379]	Numerical Solver
SVDetect	0.8b	[380]	Biology, NGS, SNP
swak4Foam	2.x	[381]	Fluid Dynamics
swarm	1.2.11	[382]	Data Analysis
Swig	2.0.9	[383]	Programming, C, C++, Python
SwitchSeq	20140907	[384]	Biology, NGS
Syzygy	1.2.7	[385]	Biology, Genomics
TASSEL	5.0	[386]	Biology, Genomics
TAU	2.21.4, 2.23	[387]	Profiling, Tracing, Programming
T-Coffee	9.03.r1318	[388]	Biology, Genomics, Multiple Alignment
TESS	2.3.1	[389]	Biology, Genomics, Markov
tgicl	2.1	[390]	Biology, sequencing, clustering
TomoPy	0.0.3	[391]	Biology, Neuroimaging
Tophat	1.4.1, 2.0.13	[392]	Biology, NGS
Totalview	8.12.0	[393]	Computer Science
TPP	4.7.0	[394]	Bioinformatics, MassSpec
TrackTools	2011	[395]	Bioinformatics
TrackVis	0.5.2.2	[396]	Biology, Spectroscopy
Tracula	5.3.2014_05_26	[397]	Biology, Bioinformatics, Neuroscience, Imaging
TraitRate	1.1	[398]	Biology, Evolution
TransDecoder	20140704	[399]	Biology, NGS
TreeFix	1.1.7	[400]	Biology, Phylogenetics
TRF	4.04	[401]	Biology, Genomics
Trilinos	11.4.1, 11.8.1	[402]	Math Algorithm
Trim Galore	0.2.8	[403]	Biology, NGS
Trimmomatic	0.22, 0.32	[404]	Biology, NGS
Trinity	r20131110, r20140413	[405]	Biology, NGS, RNA-Seq
TRNAscan-SE	1.23	[406]	Biology, NGS, Bioinformatics
Twinscan	4.1.2	[407]	Biology, Genomics
usearch	7.0.1001-64, 8.0.1517	[408]	Biology, Sequence analysis
UDUNITS	2.2.17	[409]	Library, Units, Programming
UNAFold	3.8	[410]	Biology, Genome, RNA, Folding
Valgrind	3.9.0	[411]	Computer Science
VASP	4.6.34, 5.2.12, 5.3.2, 5.3.3, 5.3.5	[412]	Quantum Chemistry, Ab Initio
VarScan	2.3.6	[413]	Biology, NGS, Genomics
VCFLib	20121207	[414]	Biology, NGS, Genomics
VCFtools	0.1.9, 0.1.10	[415]	Biology, SNPs
velvet	1.2.06, 1.2.07, 1.2.10	[416]	Biology, Genomics, NGS
VEP	74	[417]	Biology, NGS
Vim	7.4.5-minimal, 7.4.5-py2, 7.4.5	[418]	Programming, Scripting, Language
vmd	1.9.1	[419]	Biology, Visualization
VTK	6.1.0	[420]	Visualization, Graphics
Wannier90	1.2, 2.0.0	[421]	Computational Physics
WebLogo	3.3	[422]	Biology, Genomics
WDSSII	1	[423]	Meteorology
WIEN2k	12.1	[424]	Material Science, Chemistry
Wgs or Celera	7.0.1.22	[425]	Biology, NGS
wublast	2.0	[426]	Biology, Sequence Alignment
YAHA	0.1.82	[427]	Biology NGS
XCrySDen	1.5.60	[428]	Computational Material Science
Yambo	3.3.0	[429]	Physics
Yasra	2.32	[430]	Biology, NGS

To add a documentation page for a new piece of software installed into /apps please go to Add New App Page.