Installed Software

Installed Software List

Last updated 2013-10-30.

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	1.3.3, 1.3.4, 1.3.4-mpi	[2]	Biology, NGS
ALLPATHS-LG	42316, 44837	[3]	Biology, NGS
AFNI	2011_12_21_1014	[4]	Biology, Statistics, Imaging, Neurology
Amber	11, 12	[5]	Simulation, chemistry
AMOS	3.1.0	[6]	Biology, Genomics, NGS
ANNOVAR	20120621,20121023,20130321	[7]	Biology, Genomics
Amuse	6.0	[8]	Astrophysics
Affymetrix Power Tools	1.15.0	[9]	Biology, Genomics, Microarray
Augustus	2.6	[10]	Biology, NGS
Bamtools	2.1.1	[11]	Biology, NGS
BamUtil	1.0.2	[12]	Biology, NGS
BayesRate	1.3.43	[13]	Biology, Phylogenetics
Bbcp	12.08.17.00.0	[14]	Network file transfer
BEAGLE	3.2.2	[15]	Biology, Genetics, Genotyping
BEAST	1.7.5, 2.0.1, 2.0.2.pre	[16]	Biology, Phylogenetics
BEDTools	2.16.2	[17]	Biology, NGS
BEST	2.3	[18]	Biology, Phylogenetics
BFAST	0.7.0	[19]	Biology, NGS
Bismark	0.7.4, 0.7.7	[20]	Biology, Methylation, NGS
Bioconductor	Latest	[21]	Biology, R, Statistics
BioPerl	1.006901	[22]	Biology, Perl
BioPython	1.59	[23]	Biology, Python
BLASR	20130815	[24]	Biology, NGS
NCBI BLAST	2.2.26, 2.2.27, 2.2.28	[25]	Biology, Sequence alignment
Blast2go	2.5.0-20120705	[26]	Biology, Annotation
BLAT	20120524	[27]	Biology, Sequence alignment
Boost	1.49.0, 1.53.0, 1.54.0	[28]	C++, Library
Bwa	0.6.1, 0.7.2	[29]	Biology, NGS
Bowtie	0.12.8, 0.12.9, 2.1.0	[30]	Biology, NGS
CAP3	20120705	[31]	Biology, sequence assembly
CASAVA	1.8.2	[32]	Biology, NGS
CD-HIT	4.6	[33]	Biology, Genomics
CDO	1.6.1	[34]	Climate
CellProfiler	2.0	[35]	Biology, Image Analysis
Charmm	36a3	[36]	Simulation, Chemistry
Circos	0.63-pre11	[37]	Biology, Visualization
CisGenome	2.0	[38]	Biology, Genomics, Peak Calling
ClustalW	2.1	[39]	Biology, Genomics
Clview	20130402	[40]	Biology, Genomics
CMake	2.8.8	[41]	Programming, Build System
Consed	23.0	[42]	Biology, Genomics
CUDA	4.2, 5.5	[43]	Programming, Graphics
Cufflinks	1.3.0, 2.0.0, 2.0.2	[44]	Biology, NGS
Cutadapt	1.1	[45]	Biology, NGS
Desmond	3.0.3.1	[46]	Simulation, Biology, Chemistry
Dalton	2011	[47]	Quantum Chemistry
Dindel	1.01	[48]	Biology, NGS
DIYABC	many	[49]	Biology, Genomics
Dlpoly	4.03.4	[50]	Simulation, Biology, Chemistry
DNA Clust	3.0	[51]	Biology, Genomics
Dock	6.5, 6.6	[52]	Chemistry, ligand binding prediction
DTI-TK	2.3.1	[53]	Biology, Neurology, Imaging
EIGENSOFT	4.2, 5.0.1	[54]	Biology, Population
emboss	6.5.7	[55]	Biology, multi-tool suite
Espresso	5.0.1	[56]	Modeling, Physics
ESPRIT	201211	[57]	Biology, NGS, Metagenomics
ETE2	2.1	[58]	Biology, Phylogenetics
Eval	2.2.8	[59]	Biology, Genomics, GUI
ExaML	20130314	[60]	Biology, Phylogenetics
Exonerate	2.2.0	[61]	Biology, Genomics
FAR	2.15	[62]	Biology, Genomics
FASTA	34.26.5	[63]	Biology, Genomics
FastML	3.0	[64]	Biology, Phylogenetics, ML
FastQC	0.9.6, 0.10.1	[65]	Biology, NGS
Fastx_toolkit	0.0.13.2	[66]	Biology, NGS
Ferret	6.82	[67]	Oceanography, Meteorology
FFTW	3.3.2	[68]	Math, Library, C++
Fluent	14.5.7	[69]	Simulation, Fluid Dynamics
FragGeneScan	1.16	[70]	Biology, NGS, Genomics
FreeBayes	0.9.6	[71]	Biology, NGS, SNP Calling
FSL	5.0.2.2	[72]	Biology, Neurology, Imaging
Garli	2.0	[73]	Biology, Phylogenetics
GATK	1.6.9, 2.2.15, 2.6.5	[74]	Biology, NGS
Gaussian	E01, G03, G09-A.02, G09-C.01	[75]	Modeling, Computational Chemistry
GeneMark	2012.04	[76]	Biology, Genomics, Metagenomics
Genewise	2.2.0	[77]	Biology, Genomics, Annotation
GenomicTools	2.7.0	[78]	Biology, NGS
Git	1.8.2.1	[79]	Development, Revision Control
Gmap	20120712, 20130331, 20130618	[80]	Biology, Genomics
GnuPlot	4.6.0	[81]	Graphics, Plotting, Programming
Grace	5.1.22	[82]	Graphics, plotting, 2D
GrADS	2.0.1	[83]	Earth Science
Gromacs	4.5.5	[84]	Chemistry, Modeling, Simulation
GSL	1.15	[85]	Library, Math, C++, C
GULP	4.0	[86]	Material Science
HaMStR	v8b	[87]	Biology, Genomics
HDF5	1.8.9	[88]	Library, Data
HMMER3	3.0	[89]	Biology, Genomics
HOMER	4.2	[90]	Biology, Genomics
HTSeq	0.5.3p3	[91]	Biology, NGS
HyPhy	2.1.2.28	[92]	Biology, Phylogenetics
Hypre	2.8.0b	[93]	Library, Math, Physics
IDBA-UD	1.0.9, 1.1.0	[94]	Biology, NGS
IM and IMa	20091217	[95]	Biology, Population
IMa2	20120827	[96]	Biology, Population
Intel Compilers	11.1, 2012	[97]	Programming, Compilers
IOAPI	3.1	[98]	Meteorology
Iprscan	4.8	[99]	Biology, Genomics
LS-DYNA	610	[100]	Physics
ITK	4.3.1	[101]	Biology, Genomics
JAGS	3.3.0	[102]	Statistics
Java	1.6.0_31, 1.7.0_02	[103]	Java Development Kit
Kent	20120524	[104]	Biology, NGS
Kmer	1934	[105]	Biology, NGS
LAMMPS	28Oct12	[106]	Molecular Dynamics Simulation
Last	193, 247	[107]	Biology, Sequence alignment
Lastz	1.03.02, 1.02.00	[108]	Biology, NGS
LIBSVM	3.12	[109]	Machine Learning
LSC	0.3	[110]	Biology, NGS, Error correction
MACS	1.4.2	[111]	Biology, ChIP-Seq
mafft	7.037, 6.903	[112]	Biology, Multiple sequence alignment
Maker	2.10, 2.25b	[113]	Biology, Annotation, Genomics
Maq	0.7.1	[114]	Biology, NGS
Matlab	2012a	[115]	Math, Simulation, Programming
MATS	2.1.0, 3.0.6b, 3.0.8	[116]	BIology, NGS
Mauve	2.3.1	[117]	Biology, Genomics, Multiple genome alignments
MCNP	5, 6b2	[118]	Physics
MCNPX	2.7.0, 2.7.0-i8	[119]	Physics
Meme	4.8.1	[120]	Biology, Motifs, Sequence analysis
Mercurial	2.7	[121]	Development, Revision Control
Metabin	1.0	[122]	Biology, Metagenomics
MetaCluster	5.0beta	[123]	Biology, Metagenomics
MetaVelvet	1.2.01	[124]	Biology, NGS
MetaGeneMark	2012.04	[125]	Biology, Genomics
Mfold	3.6	[126]	Biology, Genomics
Midnight Commander	4.6.1	[127]	Tools, Utilities
Migrate-n	3.3.0	[128]	Biology, Population
mira	3.2.0, 3.4.0.1, 3.9.9, 3.9.18, 4.0.rc1	[129]	Biology, NGS
MISO	0.4.4	[130]	Biology, NGS
MSMBuilder	2.5.1	[131]	Molecular Dynamics
Molden	5.0	[132]	Molecular, electronic structure
mosaik	2.1.33	[133]	Biology,NGS
Mothur	1.31.2	[134]	Biology, Microbial Ecology
MrBayes	3.2.1	[135]	Biology, Phylogenetics
MUMmer	3.23	[136]	Biology, Genomics
MUSCLE	3.8.31	[137]	Biology, Genomics
NAMD	2.9	[138]	Simulation, Chemistry, Biology
Nbody	6	[139]	Astronomy
NCO	4.2.1	[140]	Data exchange tools
NetCDF	4.2	[141]	Data exchange, Tools
Newbler	2.6, 2.7	[142]	Biology, NGS
NMRPipe	7.9	[143]	Biology, Biochemistry
Novoalign	2.08.02, 3.00.02	[144]	Biology, NGS
Oases	0.2.08	[145]	Biology, NGS
Olego	1.1.2	[146]	Biology, NGS, RNA-Seq
Octave	3.6.4	[147]	Numerical Computation
OpenBabel	2.3.2	[148]	Biology, Chemistry
OpenFOAM	2.1.1	[149]	Fluid Dynamics
OrthoMCL	2.0.2, 2.0.3, 2.0.7	[150]	Biology, Genomics
PAML	4.7	[151]	Biology, Phylogenetics
PartitionFinder	1.0.1	[152]	Biology, Phylogenetics, Evolution
Parflow	v615	[153]	Ecology, Modeling
PASA	1.5, 2.0-r20130605p1, 2.0-r20130907	[154]	Biology, Genomics
PeakSplitter	1.0	[155]	Biology, Chip-Seq
PDT	3.18	[156]	Programming, Profiler
Perl	5.16.0	[157]	Programming, Language
PerM	0.4.0	[158]	Biology, NGS
PETSc	2.3, 3.3	[159]	Math, Numerical solvers
Phenix	1.8.1069	[160]	Crystallography
PHITS	2.52	[161]	Physics
PhyloBayes	3.3f, 1.4f MPI	[162]	Biology, Phylogenetics
PhyML	3.0, 20121109	[163]	Biology, Phylogenetics
Picard	1.69, 1.72, 1.80	[164]	Biology, NGS
Proteinortho	4.26	[165]	Biology, Genomics
python	2.6.8, 2.7.3	[166]	Programming, scripting, language
QIIME	1.5.0	[167]	Biology, Ecology
QT	4.8.3	[168]	Computer Science
R	2.15.1, 2.15.0-mpi, Rmpi/2.15.1, 3.0.0	[169]	Statistics, Programming
R8S	1.71	[170]	Biology, Evolution
RADICAL	0.2	[171]	Biology, Phylogenetics, Genomics
RAxML	7.3.2.0705	[172]	Biology, Phylogenetics
RepeatMasker	3.3.0	[173]	Biology, Genomics
Reptile	1.1	[174]	Biology, NGS, error correction
riboPicker	0.4.3	[175]	Biology, Sequence
RSEG	0.4.8	[176]	Biology, NGS
samtools	0.1.16, 0.1.18, 0.1.19	[177]	Biology, NGS
SAS	9.3	[178]	Statistics, Graphing
SATe	2.2.7	[179]	Biology, Phylogenetics
Sharcgs	1.2.11	[180]	Biology, NGS, de novo assembly
Schrodinger	2012, 2013	[181]	Simulation, chemistry
SCons	2.3.0	[182]	Programming, Build System
SeqPrep	0.5	[183]	Biology, NGS
SEQuel	1.0.1	[184]	Biology, NGS
Sickle	1.200	[185]	Biology, NGS, quality filter
Siesta	2.0.2,3.1	[186]	Simulation, Physics, Ab Initio
SIFT	4.0.3b	[187]	Biology, Genomics
Silo	4.7	[188]	Library, Data
Snap	20100728	[189]	Biology, Genomics
SOAPdenovo	1.05	[190]	Biology, NGS
SOAPdenovo-Trans	1.01	[191]	Biology, NGS
Spades	2.5.0, 2.5.1	[192]	Biology, NGS
Spanki	0.4.1	[193]	Biology, NGS, RNA-Seq
SPARTA+	2.60	[194]	Chemistry
SPIMAP	1.1	[195]	Biology, Phylogenetics
SpliceTrap	0.90.5	[196]	Biology, NGS, RNA-Seq
SPM	8	[197]	Biology, Statistics, Neurology, Imaging
Sputnik	1.0	[198]	Biology, Genomics
SRA	2.1.10	[199]]	biology, NGS
SSPACE	2.0	[200]	Biology, NGS
Stacks	0.9995	[201]	Biology, Genomics, NGS
Stata	10.1	[202]	Statistics, Data analysis
Structure	2.3.3, 2.3.4	[203]	Biology, Population
SUNDIALS	2.5.0	[204]	Numerical Solver
swak4Foam	2.x	[205]	Fluid Dynamics
Swig	2.0.9	[206]	Programming, C, C++, Python
TAU	2.21.4	[207]	Profiling, Tracing, Programming
T-Coffee	9.03.r1318	[208]	Biology, Genomics, Multiple Alignment
tgicl	2.1	[209]	Biology, sequencing, clustering
Tophat	1.4.1, 2.0.1, 2.0.8b	[210]	Biology, NGS
TreeFix	1.1.7	[211]	Biology, Phylogenetics
TRF	4.04	[212]	Biology, Genomics
Trilinos	11.4.1	[213]	Math Algorithm
Trimmomatic	0.22	[214]	Biology, NGS
Trinity	r20120905, r20121005, r20120225	[215]	Biology, NGS, RNA-Seq
Twinscan	4.1.2	[216]	Biology, Genomics
usearch	5.2.32, 7.0.959	[217]	Biology, Sequence analysis
VASP	4.6.34, 5.2.12, 5.3.2	[218]	Quantum Chemistry, Ab Initio
VCFtools	0.1.9, 0.1.10	[219]	Biology, SNPs
velvet	1.2.06, 1.2.07, 1.2.10	[220]	Biology, NGS
vmd	1.9.1	[221]	Biology, Visualization
WebLogo	3.3	[222]	Biology, Genomics
WDSSII	1	[223]	Meteorology
WIEN2k	12.1	[224]	Material Science, Chemistry
wgs	7.0.1.22	[225]	Biology, NGS
wublast	2.0	[226]	Biology, Sequence Alignment
Yambo	3.3.0	[227]	Physics
Yasra	2.32	[228]	Biology, NGS

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