Installed Software

Installed Software List

Last updated 2013-04-22.

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
Amber	11, 12	[4]	Simulation, chemistry
Amuse	6.0	[5]	Astrophysics
Affymetrix Power Tools	1.15.0	[6]	Biology, Genomics, Microarray
Augustus	2.6	[7]	Biology, NGS
Bamtools	2.1.1	[8]	Biology, NGS
BamUtil	1.0.2	[9]	Biology, NGS
BayesRate	1.3.43	[10]	Biology, Phylogenetics
Bbcp	12.08.17.00.0	[11]	Network file transfer
BEAST	1.7.5, 2.0.1, 2.0.2.pre	[12]	Biology, Phylogenetics
BEDTools	2.16.2	[13]	Biology, NGS
BEST	2.3	[14]	Biology, Phylogenetics
BFAST	0.7.0	[15]	Biology, NGS
Bismark	0.7.4, 0.7.7	[16]	Biology, Methylation, NGS
Bioconductor	Latest	[17]	Biology, R, Statistics
BioPerl	1.006901	[18]	Biology, Perl
BioPython	1.59	[19]	Biology, Python
NCBI BLAST	2.2.26 (+ and legacy)	[20]	Biology, Sequence alignment
Blast2go	2.5.0-20120705	[21]	Biology, Annotation
BLAT	20120524	[22]	Biology, Sequence alignment
Boost	1.49.0	[23]	C++, Library
Bwa	0.6.1, 0.7.2	[24]	Biology, NGS
Bowtie	0.12.8, 0.12.9, 2.1.0	[25]	Biology, NGS
CAP3	20120705	[26]	Biology, sequence assembly
CASAVA	1.8.2	[27]	Biology, NGS
CD-HIT	4.6	[28]	Biology, Genomics
CellProfiler	2.0	[29]	Biology, Image Analysis
Charmm	36a3	[30]	Simulation, Chemistry
Circos	0.63-pre11	[31]	Biology, Visualization
CisGenome	2.0	[32]	Biology, Genomics, Peak Calling
ClustalW	2.1	[33]	Biology, Genomics
CMake	2.8.8	[34]	Programming
Consed	23.0	[35]	Biology, Genomics
CUDA	4.2	[36]	Programming, Graphics
Cufflinks	1.3.0, 2.0.0, 2.0.2	[37]	Biology, NGS
Cutadapt	1.1	[38]	Biology, NGS
Desmond	3.0.3.1	[39]	Simulation, Biology, Chemistry
Dindel	1.01	[40]	Biology, NGS
DIYABC	many	[41]	Biology, Genomics
Dlpoly	4.03.4	[42]	Simulation, Biology, Chemistry
Dock	6.5, 6.6	[43]	Chemistry, ligand binding prediction
DTI-TK	2.3.1	[44]	Bioinformatics, Neurology, Imaging
emboss	6.5.7	[45]	Biology, multi-tool suite
Espresso	5.0.1	[46]	Modeling, Physics
ESPRIT	201211	[47]	Biology, NGS, Metagenomics
ETE2	2.1	[48]	Biology, Phylogenetics
Eval	2.2.8	[49]	Biology, Genomics, GUI
ExaML	20130314	[50]	Biology, Phylogenetics
Exonerate	2.2.0	[51]	Biology, Genomics
FAR	2.15	[52]	Biology, Genomics
FASTA	34.26.5	[53]	Biology, Genomics
FastQC	0.9.6, 0.10.1	[54]	Biology, NGS
Fastx_toolkit	0.0.13.2	[55]	Biology, NGS
Ferret	6.82	[56]	Oceanography, Meteorology
FFTW	3.3.2	[57]	Math, Library, C++
FragGeneScan	1.16	[58]	Biology, NGS, Genomics
FreeBayes	0.9.6	[59]	Biology
FSL	5.0.2.2	[60]	Biology, Neurology, Imaging
Garli	2.0	[61]	Biology, Phylogenetics
GATK	1.6.9	[62]	Biology, NGS
Gaussian	E01, G03, G09-A.02, G09-C.01	[63]	Modeling, Computational Chemistry
GeneMark	2012.04	[64]	Biology, Genomics, Metagenomics
Genewise	2.2.0	[65]	Biology, Genomics, Annotation
GenomicTools	2.7.0	[66]	Biology, NGS
Gmap	20070928, 20120712	[67]	Biology, Genomics
GnuPlot	4.6.0	[68]	Graphics, Plotting, Programming
Grace	5.1.22	[69]	Graphics, plotting, 2D
GrADS	2.0.1	[70]	Earth Science
Gromacs	4.5.5	[71]	Chemistry, Modeling, Simulation
GSL	1.15	[72]	Library, Math, C++, C
HaMStR	v8b	[73]	Biology, Genomics
HDF5	1.8.9	[74]	Library, Data
HMMER3	3.0	[75]	Biology, Genomics
HTSeq	0.5.3p3	[76]	Biology, NGS
HyPhy	2.1.2.28	[77]	Biology, Phylogenetics
Hypre	2.8.0b	[78]	Library, Math, Physics
IDBA-UD	1.0.9, 1.1.0	[79]	Biology, NGS
IM and IMa	20091217	[80]	Biology, Population
IMa2	20120827	[81]	Biology, Population
Intel Compilers	11.1, 2012	[82]	Programming, Compilers
Iprscan	4.8	[83]	Biology, Genomics
ITK	4.3.1	[84]	Biology, Genomics
JDK	1.6.0_31, 1.7.0_02	[85]	Java Development Kit
Kent	20120524	[86]	Biology, NGS
Kmer	1934	[87]	Biology, NGS
LAMMPS	28Oct12	[88]	Molecular Dynamics Simulation
Last	193, 247	[89]	Biology, Sequence alignment
Lastz	1.03.02, 1.02.00	[90]	Biology, NGS
LIBSVM	3.12	[91]	Machine Learning
MACS	1.4.2	[92]	Biology, ChIP-Seq
mafft	6.903	[93]	Biology, Multiple sequence alignment
Maker	2.10, 2.25b	[94]	Biology, Annotation, Genomics
Maq	0.7.1	[95]	Biology, NGS
Matlab	2012a	[96]	Math, Simulation, Programming
MATS	2.1.0, 3.0.4, 3.0.6	[97]	BIology, NGS
MCNP	5, 6b2	[98]	Physics
MCNPX	2.7.0, 2.7.0-i8	[99]	Physics
Meme	4.8.1	[100]	Biology, Motifs, Sequence analysis
MetaCluster	5.0beta	[101]	Biology
MetaVelvet	1.2.01	[102]	Biology, NGS
MetaGeneMark	2012.04	[103]	Biology, Genomics
Midnight Commander	4.6.1	[104]	Tools, Utilities
Migrate-n	3.3.0	[105]	Biology, Population
mira	3.2.0, 3.4.0.1	[106]	Biology, NGS
MISO	0.4.4	[107]	Biology, NGS
MSMBuilder	2.5.1	[108]	Molecular Dynamics
Molden	5.0	[109]	Molecular, electronic structure
mosaik	2.1.33	[110]	Biology,NGS
MrBayes	3.2.1	[111]	Biology, Phylogenetics
MUMmer	3.23	[112]	Biology, Genomics
MUSCLE	3.8.31	[113]	Biology, Genomics
NAMD	2.9	[114]	Simulation, Chemistry, Biology
Nbody	6	[115]	Astronomy
NCO	4.2.1	[116]	Data exchange tools
NetCDF	4.2	[117]	Data exchange, Tools
Newbler	2.6, 2.7	[118]	Biology, NGS
Novoalign	2.08.02, 3.00.02	[119]	Biology, NGS
Oases	0.2.08	[120]	Biology, NGS
Octave	3.6.4	[121]	Numerical Computation
OpenFOAM	2.1.1	[122]	Fluid Dynamics
OrthoMCL	2.0.2, 2.0.3, 2.0.7	[123]	Biology, Genomics
PartitionFinder	1.0.1	[124]	Biology, Phylogenetics, Evolution
Parflow	v615	[125]	Ecology, Modeling
PASA	1.5, r20120625	[126]	Biology, Genomics
PeakSplitter	1.0	[127]	Biology, Chip-Seq
PDT	3.18	[128]	Programming, Profiler
Perl	5.16.0	[129]	Programming, Language
PerM	0.4.0	[130]	Biology, NGS
Phenix	1.8.1069	[131]	Crystallography
PhyloBayes	3.3f	[132]	Biology, Phylogenetics
PhyML	3.0, 20121109	[133]	Biology, Phylogenetics
Picard	1.69, 1.72, 1.80	[134]	Biology, NGS
Proteinortho	4.26	[135]	Biology, Genomics
python	2.6.8, 2.7.3	[136]	Programming, scripting, language
QIIME	1.5.0	[137]	Biology, Ecology
R	2.15.1, 2.15.0-mpi, Rmpi/2.15.1, 3.0.0	[138]	Statistics, Programming
R8S	1.71	[139]	Biology, Evolution
RADICAL	0.2	[140]	Biology, Phylogenetics, Genomics
RAxML	7.3.2.0705	[141]	Biology, Phylogenetics
RepeatMasker	3.3.0	[142]	Biology, Genomics
Reptile	1.1	[143]	Biology, NGS, error correction
riboPicker	0.4.3	[144]	Biology, Sequence
RSEG	0.4.8	[145]	Biology, NGS
samtools	0.1.16, 0.1.18, 0.1.19	[146]	Biology, NGS
SAS	9.3	[147]	Statistics, Graphing
SATe	2.2.7	[148]	Biology, Phylogenetics
Schrodinger	2012	[149]	Simulation, chemistry
SeqPrep	0.5	[150]	Biology, NGS
SEQuel	1.0.1	[151]	Biology, NGS
Sickle	1.200	[152]	Biology, NGS, quality filter
Siesta	2.0.2,3.1	[153]	Simulation, Physics, Ab Initio
SIFT	4.0.3b	[154]	Biology, Genomics
Silo	4.7	[155]	Library, Data
Snap	20100728	[156]	Biology, Genomics
SOAPdenovo	1.05	[157]	Biology, NGS
SOAPdenovo-Trans	1.01	[158]	Biology, NGS
SPARTA+	2.60	[159]	Chemistry
SPIMAP	1.1	[160]	Biology, Phylogenetics
SpliceTrap	0.90.5	[161]	Biology, NGS, RNA-Seq
Sputnik	1.0	[162]	Biology, Genomics
SRA	2.1.10	[163]]	biology, NGS
SSPACE	2.0	[164]	Biology, NGS
Stacks	0.9995	[165]	Biology, Genomics, NGS
Structure	2.3.3	[166]	Biology, Population
Swig	2.0.9	[167]	Programming, C, C++, Python
TAU	2.21.4	[168]	Profiling, Tracing, Programming
tgicl	2.1	[169]	Biology, sequencing, clustering
Tophat	1.4.1, 2.0.1	[170]	Biology, NGS
TreeFix	1.1.7	[171]	Biology, Phylogenetics
TRF	4.04	[172]	Biology, Genomics
Trimmomatic	0.22	[173]	Biology, NGS
Trinity	r20120905, r20121005, r20120225	[174]	Biology, RNA-Seq
Twinscan	4.1.2	[175]	Biology, Genomics
usearch	5.2.32	[176]	Biology, Sequence analysis
VASP	4.6.34, 5.2.12, 5.3.2	[177]	Quantum Chemistry, Ab Initio
VCFtools	0.1.9, 0.1.10	[178]	Biology, SNPs
velvet	1.2.06, 1.2.07	[179]	Biology, NGS
vmd	1.9.1	[180]	Biology, Visualization
WebLogo	3.3	[181]	Biology, Genomics
WDSSII	1	[182]	Meteorology
WIEN2k	12.1	[183]	Material Science, Chemistry
wgs	7.0.1.22	[184]	Biology, NGS
wublast	2.0	[185]	Biology, Sequence Alignment
Yasra	2.32	[186]	Biology, NGS

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