Installed Software

Installed Software List

Last updated 2014-08-08.

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

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
ALLPATHS-LG	42316, 44837	[3]	Biology, NGS
AFNI	2011_12_21_1014	[4]	Biology, Statistics, Imaging, Neurology
Amber	11, 12, 14	[5]	Simulation, chemistry
AMOS	3.1.0	[6]	Biology, Genomics, NGS
ANNOVAR	20120621,20121023,20130321	[7]	Biology, Genomics
Atlas	3.10.1, 3.11.17	[8]	Library, Math
Amuse	6.0	[9]	Astrophysics
Affymetrix Power Tools	1.15.0	[10]	Biology, Genomics, Microarray
AtomEye	3	[11]	Material Science
ATRAM	20140624	[12]	Biology, NGS
Augustus	2.6	[13]	Biology, NGS
BamBam	1.0	[14]	Biology, NGS
Bamstats	20140602	[15]	Biology, NGS
Bamtools	2.1.1	[16]	Biology, NGS
BamUtil	1.0.2	[17]	Biology, NGS
BayesRate	1.3.43	[18]	Biology, Phylogenetics
Bbcp	12.08.17.00.0	[19]	Network file transfer
Bcftools	20140618	[20]]	Biology, Genomics, NGS
BEAGLE	3.2.2	[21]	Biology, Genetics, Genotyping
BEAST	1.7.5, 2.0.1, 2.0.2.pre	[22]	Biology, Phylogenetics
BEDTools	2.16.2, 2.17.0	[23]	Biology, NGS
BEST	2.3	[24]	Biology, Phylogenetics
BETA	1.0.5	[25]	Biology, NGS
BFAST	0.7.0	[26]	Biology, NGS
Bismark	0.7.4, 0.7.7	[27]	Biology, Methylation, NGS
Bioconductor	Latest	[28]	Biology, R, Statistics
BioPerl	1.006901	[29]	Biology, Perl
BioPython	1.59	[30]	Biology, Python
BLASR	20130815	[31]	Biology, NGS
NCBI BLAST	2.2.27, 2.2.28, 2.2.29	[32]	Biology, Sequence alignment
Blast2go	2.5.0-20120705	[33]	Biology, Annotation
BLAT	20120524	[34]	Biology, Sequence alignment
Blender	2.63	[35]	Graphics
Boost	1.49.0, 1.53.0, 1.54.0	[36]	C++, Library
Bowtie	0.12.8, 0.12.9, 1.0.0	[37]	Biology, NGS
Bowtie2	2.1.0, 2.2.2, 2.2.3	[38]	Biology, NGS
BRANCH	1.8.1	[39]	Biology, NGS, Mapping
Bwa	0.6.1, 0.7.9a, 0.7.10	[40]	Biology, NGS
Camino	20140723	[41]	Biology, Neuroscience, Imaging
CAP3	20120705	[42]	Biology, sequence assembly
CASAVA	1.8.2	[43]	Biology, NGS
CD-HIT	4.6	[44]	Biology, Genomics
CDO	1.6.1	[45]	Climate
CEAS	1.0.2	[46]	Biology, Genomics
CellProfiler	2.0	[47]	Biology, Image Analysis
Charmm	36a3	[48]	Simulation, Chemistry
Chartdirector	5.1.0	[49]	Graphics
CIMS	4.1.2	[50]	Biology, Genomics
Circos	0.63-pre11	[51]	Biology, Visualization
CisGenome	2.0	[52]	Biology, Genomics, Peak Calling
CLHEP	2.2.0.1	[53]	High Energy Physics
ClonalFrame	1.1, 1.2	[54]	Biology, Genomics, NGS
ClustalW	2.1	[55]	Biology, Genomics
Clview	20130402	[56]	Biology, Genomics
CMake	2.8.8	[57]	Programming, Build System
CNVSeq	20110715	[58]	Biology, NGS
Coevol	1.3c, 1.4b	[59]	Biology, Phylogenetics
CoMap	1.4.1	[60]	Biology, Genomics
CONCOCT	0.3.1	[61]	Biology, Genomics
Consed	23.0	[62]	Biology, Genomics
covNMR	2014	[63]	Biochemistry
CUDA	4.2, 5.5	[64]	Programming, Graphics
Cufflinks	1.3.0, 2.0.2, 2.2.1	[65]	Biology, NGS
Cutadapt	1.1	[66]	Biology, NGS
DAKOTA	5.4.0	[67]	Computational Science
DCMTK	3.6.0	[68]	Biology, Neuroscience, Imaging
DDSCAT	7.3.0	[69]	Astrophysics
DDT	4.1.0, 4.2.1	[70]	Software
Delft3D	3621	[71]	Hydrodynamics, Physics
Desmond	3.0.3.1	[72]	Simulation, Biology, Chemistry
Dalton	2011	[73]	Quantum Chemistry
DiffReps	1.55.4	[74]	Biology, NGS, ChIP-Seq
Dindel	1.01	[75]	Biology, NGS
DIYABC	many	[76]	Biology, Genomics
Dlpoly	4.03.4	[77]	Simulation, Biology, Chemistry
DNA Clust	3.0	[78]	Biology, Genomics
Dock	6.5, 6.6	[79]	Chemistry, ligand binding prediction
DOT	2.0	[80]	Biology, Bioinformatics, Docking
Doxygen	1.8.3.1	[81]	Programming, Documentation
DSSP	2.2.1	[82]	Biology, Molecular Dynamics
DTI-TK	2.3.1	[83]	Biology, Neurology, Imaging
EA-Utils	1.1.2.537	[84]	Biology, NGS
ECTools	20140311	[85]	Biology, Sequencing, Bioinformatics
EIGENSOFT	4.2, 5.0.1	[86]	Biology, Population
emboss	6.5.7	[87]	Biology, multi-tool suite
eQTLA	1.1	[88]	Biology, Genomics
Espresso	5.0.1	[89]	Modeling, Physics
ESPRIT	201211	[90]	Biology, NGS, Metagenomics
ETE2	2.1	[91]	Biology, Phylogenetics
Eval	2.2.8	[92]	Biology, Genomics, GUI
ExaML	1.0.3, 1.0.5, 1.0.12	[93]	Biology, Phylogenetics
Exonerate	2.2.0	[94]	Biology, Genomics
FAR	2.15	[95]	Biology, Genomics
FASTA	34.26.5, 36.3.6d	[96]	Biology, Genomics
FastML	3.0	[97]	Biology, Phylogenetics, ML
FastQC	0.9.6, 0.10.1	[98]	Biology, NGS
FastTree	2.1.7	[99]	Biology, Phylogenetics
Fastx_toolkit	0.0.13.2	[100]	Biology, NGS
fcGENE	1.0.7	[101]	Biology, Genomics, SNP
Ferret	6.82	[102]	Oceanography, Meteorology
FFmpeg	2.1.3	[103]	Multimedia, audio, video
FFTW	3.3.2, 3.3.3	[104]	Math, Library, C++
FLASH	1.2.10	[105]	Biology, Genomics, NGS
Fluent	14.5.7, 15.0	[106]	Simulation, Fluid Dynamics
FragGeneScan	1.16	[107]	Biology, NGS, Genomics
FreeBayes	0.9.6	[108]	Biology, NGS, SNP Calling
Freesurfer	5.2.0	[109]	Biology, Neurology, Imaging
FSL	5.0.2.2	[110]	Biology, Neurology, Imaging
Garli	2.0, 2.01	[111]	Biology, Phylogenetics
GASVPro	201310	[112]	Biology, NGS, Genomics
GATE	7.0	[113]	Data Analysis
GATK	1.6.9, 2.7.4, 3.1.1	[114]	Biology, NGS
Gaussian	E01, G03, G09-A.02, G09-C.01	[115]	Modeling, Computational Chemistry
Geant4	4.10	[116]	Physics
GEM	20130406	[117]	Biology, NGS
GEMINI	4.6.6a	[118]	Biology, Genomics, Genetics
GenBank Tools	20140130	[119]	BIology< Genomics
GeneMark	2012.04	[120]	Biology, Genomics, Metagenomics
Genewise	2.2.0	[121]	Biology, Genomics, Annotation
GenomicTools	2.7.0	[122]	Biology, NGS
Git	1.8.2.1	[123]	Development, Revision Control
Gmap	20130618, 20130720, 20140530	[124]	Biology, Genomics
GnuPlot	4.6.0	[125]	Graphics, Plotting, Programming
Grace	5.1.22	[126]	Graphics, plotting, 2D
GrADS	2.0.1	[127]	Earth Science
GraphViz	2.38.0	[128]	Graphics, plotting, visualization
Gromacs	4.5.5, 4.6.5	[129]	Chemistry, Modeling, Simulation
GSL	1.15	[130]	Library, Math, C++, C
GULP	4.0	[131]	Material Science
HaMStR	v8b	[132]	Biology, Genomics
Hapsembler	2.21	[133]	Biology, Genomics, NGS
HDF5	1.8.9, 1.8.12	[134]	Library, Data
HMMER3	3.0	[135]	Biology, Genomics
HMMSplicer	0.9.5	[136]	Biology, Genomics
HOMER	4.2	[137]	Biology, Genomics
HTSeq	0.5.3p3, 0.6.1p1	[138]	Biology, NGS
HyPhy	2.1.2.28	[139]	Biology, Phylogenetics
Hypre	1.10.0b, 2.8.0b	[140]	Library, Math, Physics
IDBA-UD	1.0.9, 1.1.0	[141]	Biology, NGS
IM and IMa	20091217	[142]	Biology, Population
IMa2	20120827	[143]	Biology, Population
ImageMagick	6.8.8-9	[144]	Image manipulation
Intel Compilers	11.1, 2012	[145]	Programming, Compilers
IOAPI	3.1	[146]	Meteorology
Iprscan	4.8	[147]	Biology, Genomics
ITK	4.3.1	[148]	Biology, Genomics
ITK-SNAP	3.0.0	[149]	Biology, Neuroscience, Imaging
JAGS	3.3.0	[150]	Statistics
Java	1.6.0_31, 1.7.0_02	[151]	Java Development Kit
Kent	20120524	[152]	Biology, NGS
Kmer	1934	[153]	Biology, NGS
LAMMPS	28Oct12, 30Sep13	[154]	Molecular Dynamics Simulation
Last	193, 247	[155]	Biology, Sequence alignment
Lastz	1.03.02, 1.02.00	[156]	Biology, NGS
LIBSVM	3.12	[157]	Machine Learning
LSC	0.3, 0.3.1	[158]	Biology, NGS, Error correction
Loci	3.3	[159]	Fluid Dynamics
LS-DYNA	700, 711	[160]	Physics
MACH	1.0.18	[161]	Biology, Genomics
MACS	1.4.2	[162]	Biology, ChIP-Seq
mafft	7.037, 6.903	[163]	Biology, Multiple sequence alignment
Maker	2.10, 2.25b	[164]	Biology, Annotation, Genomics
Maq	0.7.1	[165]	Biology, NGS
Matlab	2012a, 2013a, 2014a	[166]	Math, Simulation, Programming
MATS	2.1.0, 3.0.6b, 3.0.8	[167]	BIology, NGS
MCarts	1.0.2	[168]	Biology, Genomics, Markov models
MCNP	5, 6b2	[169]	Physics
MCNPX	2.7.0, 2.7.0-i8	[170]	Physics
Meme	4.8.1	[171]	Biology, Motifs, Sequence analysis
Mercurial	2.7	[172]	Development, Revision Control
Metabin	1.0	[173]	Biology, Metagenomics
MetaCluster	5.0beta	[174]	Biology, Metagenomics
MetaVelvet	1.2.01	[175]	Biology, NGS
MetaGeneMark	2012.04	[176]	Biology, Genomics
Mfold	3.6	[177]	Biology, Genomics
Midnight Commander	4.6.1	[178]	Tools, Utilities
Migrate-n	3.3.0	[179]	Biology, Population
mira	3.2.0, 3.4.0.1, 3.9.9, 3.9.18, 4.0.rc1	[180]	Biology, NGS
MISO	0.4.4, 0.4.9	[181]	Biology, NGS
MSMBuilder	2.5.1	[182]	Molecular Dynamics
Modeller	9.11, 9.13, 9.14	[183]	Biology, Modeling
Molden	5.0	[184]	Molecular, electronic structure
mosaik	2.1.33	[185]	Biology,NGS
Mothur	1.31.2	[186]	Biology, Microbial Ecology
MP-EST	1.4	[187]	Biology, Phylogenetics
mpiP	3.4.1	[188]	Parallel Computing
MrBayes	3.2.1	[189]	Biology, Phylogenetics
MRIcron	201306	[190]	Biology, MRI, Imaging
MUMmer	3.23	[191]	Biology, Genomics
MUSCLE	3.8.31	[192]	Biology, Genomics
NAMD	2.9	[193]	Simulation, Chemistry, Biology
Nbody	6	[194]	Astronomy
NCBI C++ Toolkit	12.0.0	[195]	Biology, C++, Development
NCL	6.1.2	[196]	Atmosphere Science
NCO	4.2.1, 4.4.3	[197]	Data exchange tools
NetCDF	4.2	[198]	Data exchange, Tools
Newbler	2.6, 2.7	[199]	Biology, NGS
Nexus NCL	2.1.18	[200]	Biology, Phylogenetics, Library
NMRPipe	7.9	[201]	Biology, Biochemistry
Novoalign	2.08.02, 3.00.02	[202]	Biology, NGS
Oases	0.2.08	[203]	Biology, NGS
Olego	1.1.2, 1.1.5	[204]	Biology, NGS, RNA-Seq
Octave	3.6.4	[205]	Numerical Computation
OpenBabel	2.3.2	[206]	Biology, Chemistry
OpenCV	2.4.8	[207]	Computervision
OpenFOAM	2.1.1	[208]	Fluid Dynamics
OrthoMCL	2.0.2, 2.0.3, 2.0.7	[209]	Biology, Genomics
PAML	4.7	[210]	Biology, Phylogenetics
ParaView	4.1.0	[211]	Data Analysis
PartitionFinder	1.0.1, 1.1.1	[212]	Biology, Phylogenetics, Evolution
Parflow	v615	[213]	Ecology, Modeling
PASA	1.5, 2.0-r20130605p1, 2.0-r20130907	[214]	Biology, Genomics
PeakSplitter	1.0	[215]	Biology, Chip-Seq
PDT	3.18	[216]	Programming, Profiler
Perl	5.16.0	[217]	Programming, Language
PerM	0.4.0	[218]	Biology, NGS
PETSc	2.3, 3.3	[219]	Math, Numerical solvers
Phenix	1.8.1069	[220]	Crystallography
PHITS	2.52	[221]	Physics
PhyloBayes	3.3f, 1.4f MPI	[222]	Biology, Phylogenetics
PhyML	3.0, 20121109	[223]	Biology, Phylogenetics
Picard	1.69, 1.72, 1.80	[224]	Biology, NGS
Preseq	0.0.4	[225]	Biology, NGS
ProBABEL	0.4.2	[226]	Biology, Genomics, GWAS
Proovread	1.03rcl	[227]	Biology, Genomics, NGS
Proteinortho	4.26	[228]	Biology, Genomics
python	2.6.8, 2.7.3	[229]	Programming, scripting, language
QIIME	1.5.0	[230]	Biology, Ecology
QT	4.8.3	[231]	Computer Science
Quickquartet	1.0.0	[232]	Biology, Phylogenetics
R	2.15.1, 2.15.0-mpi, Rmpi/2.15.1, 3.0.0	[233]	Statistics, Programming
R8S	1.71	[234]	Biology, Evolution
RADICAL	0.2	[235]	Biology, Phylogenetics, Genomics
RAxML	7.9.1, 8.0.0, 8.0.25	[236]	Biology, Phylogenetics
RepeatMasker	3.3.0	[237]	Biology, Genomics
Reptile	1.1	[238]	Biology, NGS, error correction
riboPicker	0.4.3	[239]	Biology, Sequence
RNAhybrid	2.1.1	[240]	Biology, Genomics
ROOT	6.0	[241]	Data Analysis
RSEG	0.4.8	[242]	Biology, NGS
Sailfish	0.6.3	[243]	Biology, NGS, RNA-Seq
samtools	0.1.16, 0.1.18, 0.1.19	[244]	Biology, NGS
SAS	9.3	[245]	Statistics, Graphing
SATe	2.2.7	[246]	Biology, Phylogenetics
Sharcgs	1.2.11	[247]	Biology, NGS, de novo assembly
Schrodinger	2012, 2013	[248]	Simulation, chemistry
SCons	2.3.0	[249]	Programming, Build System
SeqPrep	0.5	[250]	Biology, NGS
SEQuel	1.0.1	[251]	Biology, NGS
Seqtk	20140729	[252]	Biology, NGS
SeqyClean	1.8.10	[253]	Biology, NGS, quality filter
Sickle	1.200	[254]	Biology, NGS, quality filter
Siesta	2.0.2,3.1	[255]	Simulation, Physics, Ab Initio
SIFT	4.0.3b	[256]	Biology, Genomics
Silo	4.7	[257]	Library, Data
Slicer	4.3.1	[258]	Biology, Imaging
SMALT	0.7.6	[259]	Biology, NGS
Snap	20100728	[260]	Biology, Genomics
SOAPdenovo	1.05	[261]	Biology, NGS
SOAPdenovo-Trans	1.01, 1.03	[262]	Biology, NGS
SparCC	201402	[263]	Microbial Ecology
Spades	2.5.0, 2.5.1, 3.0.0	[264]	Biology, NGS
Spanki	0.4.1, 0.4.3	[265]	Biology, NGS, RNA-Seq
SPARTA+	2.60	[266]	Chemistry
SPIMAP	1.1	[267]	Biology, Phylogenetics
SpliceTrap	0.90.5	[268]	Biology, NGS, RNA-Seq
SPM	8	[269]	Biology, Statistics, Neurology, Imaging
Sputnik	1.0	[270]	Biology, Genomics
SRA	2.1.10	[271]]	biology, NGS
SSPACE	2.0	[272]	Biology, NGS
Stacks	0.9995	[273]	Biology, Genomics, NGS
STAR	2.3.0e	[274]	Biology, NGS, Alignment
STAR-CCM+	8.06	[275]	Mechanical Engineering
Stata	10.1, 13	[276]	Statistics, Data analysis
Stringtie	0.97	[277]	Biology, NGS, Alignment
Structure	2.3.3, 2.3.4	[278]	Biology, Population
SUNDIALS	2.3.0, 2.5.0	[279]	Numerical Solver
swak4Foam	2.x	[280]	Fluid Dynamics
Swig	2.0.9	[281]	Programming, C, C++, Python
Syzygy	1.2.7	[282]	Biology, Genomics
TAU	2.21.4, 2.23	[283]	Profiling, Tracing, Programming
T-Coffee	9.03.r1318	[284]	Biology, Genomics, Multiple Alignment
TESS	2.3.1	[285]	Biology, Genomics, Markov
tgicl	2.1	[286]	Biology, sequencing, clustering
Tophat	1.4.1, 2.0.1, 2.0.8b	[287]	Biology, NGS
Totalview	8.12.0	[288]	Computer Science
TPP	4.7.0	[289]	Bioinformatics, MassSpec
TreeFix	1.1.7	[290]	Biology, Phylogenetics
TRF	4.04	[291]	Biology, Genomics
Trilinos	11.4.1, 11.8.1	[292]	Math Algorithm
Trimmomatic	0.22, 0.32	[293]	Biology, NGS
Trinity	r20131110, r20140413	[294]	Biology, NGS, RNA-Seq
Twinscan	4.1.2	[295]	Biology, Genomics
usearch	5.2.32, 7.0.959, 7.0.1001-64 (licensed 64-bit)	[296]	Biology, Sequence analysis
Valgrind	3.9.0	[297]	Computer Science
VASP	4.6.34, 5.2.12, 5.3.2, 5.3.3	[298]	Quantum Chemistry, Ab Initio
VCFtools	0.1.9, 0.1.10	[299]	Biology, SNPs
velvet	1.2.06, 1.2.07, 1.2.10	[300]	Biology, NGS
vmd	1.9.1	[301]	Biology, Visualization
Wannier90	1.2, 2.0.0	[302]	Computational Physics
WebLogo	3.3	[303]	Biology, Genomics
WDSSII	1	[304]	Meteorology
WIEN2k	12.1	[305]	Material Science, Chemistry
wgs	7.0.1.22	[306]	Biology, NGS
wublast	2.0	[307]	Biology, Sequence Alignment
Yambo	3.3.0	[308]	Physics
Yasra	2.32	[309]	Biology, NGS

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