Difference between revisions of "Installed Software"

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| [[Dock]] || 6.5, 6.6 || [http://dock.compbio.ucsf.edu/] || Chemistry, ligand binding prediction
 
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[[DTI-TK]] || 2.3.1 || [http://www.nitrc.org/projects/dtitk/] || Bioinformatics, Neurology, Imaging
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| [[DTI-TK]] || 2.3.1 || [http://www.nitrc.org/projects/dtitk/] || Bioinformatics, Neurology, Imaging
 
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Revision as of 18:59, 22 April 2013

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 [1] 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
Garli 2.0 [60] Biology, Phylogenetics
GATK 1.6.9 [61] Biology, NGS
Gaussian E01, G03, G09-A.02, G09-C.01 [62] Modeling, Computational Chemistry
GeneMark 2012.04 [63] Biology, Genomics, Metagenomics
Genewise 2.2.0 [64] Biology, Genomics, Annotation
GenomicTools 2.7.0 [65] Biology, NGS
Gmap 20070928, 20120712 [66] Biology, Genomics
GnuPlot 4.6.0 [67] Graphics, Plotting, Programming
Grace 5.1.22 [68] Graphics, plotting, 2D
GrADS 2.0.1 [69] Earth Science
Gromacs 4.5.5 [70] Chemistry, Modeling, Simulation
GSL 1.15 [71] Library, Math, C++, C
HaMStR v8b [72] Biology, Genomics
HDF5 1.8.9 [73] Library, Data
HMMER3 3.0 [74] Biology, Genomics
HTSeq 0.5.3p3 [75] Biology, NGS
HyPhy 2.1.2.28 [76] Biology, Phylogenetics
Hypre 2.8.0b [77] Library, Math, Physics
IDBA-UD 1.0.9, 1.1.0 [78] Biology, NGS
IM and IMa 20091217 [79] Biology, Population
IMa2 20120827 [80] Biology, Population
Intel Compilers 11.1, 2012 [81] Programming, Compilers
Iprscan 4.8 [82] Biology, Genomics
ITK 4.3.1 [83] Biology, Genomics
JDK 1.6.0_31, 1.7.0_02 [84] Java Development Kit
Kent 20120524 [85] Biology, NGS
Kmer 1934 [86] Biology, NGS
LAMMPS 28Oct12 [87] Molecular Dynamics Simulation
Last 193, 247 [88] Biology, Sequence alignment
Lastz 1.03.02, 1.02.00 [89] Biology, NGS
LIBSVM 3.12 [90] Machine Learning
MACS 1.4.2 [91] Biology, ChIP-Seq
mafft 6.903 [92] Biology, Multiple sequence alignment
Maker 2.10, 2.25b [93] Biology, Annotation, Genomics
Maq 0.7.1 [94] Biology, NGS
Matlab 2012a [95] Math, Simulation, Programming
MATS 2.1.0, 3.0.4, 3.0.6 [96] BIology, NGS
MCNP 5, 6b2 [97] Physics
MCNPX 2.7.0, 2.7.0-i8 [98] Physics
Meme 4.8.1 [99] Biology, Motifs, Sequence analysis
MetaCluster 5.0beta [100] Biology
MetaVelvet 1.2.01 [101] Biology, NGS
MetaGeneMark 2012.04 [102] Biology, Genomics
Midnight Commander 4.6.1 [103] Tools, Utilities
Migrate-n 3.3.0 [104] Biology, Population
mira 3.2.0, 3.4.0.1 [105] Biology, NGS
MISO 0.4.4 [106] Biology, NGS
MSMBuilder 2.5.1 [107] Molecular Dynamics
Molden 5.0 [108] Molecular, electronic structure
mosaik 2.1.33 [109] Biology,NGS
MrBayes 3.2.1 [110] Biology, Phylogenetics
MUMmer 3.23 [111] Biology, Genomics
MUSCLE 3.8.31 [112] Biology, Genomics
NAMD 2.9 [113] Simulation, Chemistry, Biology
Nbody 6 [114] Astronomy
NCO 4.2.1 [115] Data exchange tools
NetCDF 4.2 [116] Data exchange, Tools
Newbler 2.6, 2.7 [117] Biology, NGS
Novoalign 2.08.02, 3.00.02 [118] Biology, NGS
Oases 0.2.08 [119] Biology, NGS
Octave 3.6.4 [120] Numerical Computation
OpenFOAM 2.1.1 [121] Fluid Dynamics
OrthoMCL 2.0.2, 2.0.3, 2.0.7 [122] Biology, Genomics
PartitionFinder 1.0.1 [123] Biology, Phylogenetics, Evolution
Parflow v615 [124] Ecology, Modeling
PASA 1.5, r20120625 [125] Biology, Genomics
PeakSplitter 1.0 [126] Biology, Chip-Seq
PDT 3.18 [127] Programming, Profiler
Perl 5.16.0 [128] Programming, Language
PerM 0.4.0 [129] Biology, NGS
Phenix 1.8.1069 [130] Crystallography
PhyloBayes 3.3f [131] Biology, Phylogenetics
PhyML 3.0, 20121109 [132] Biology, Phylogenetics
Picard 1.69, 1.72, 1.80 [133] Biology, NGS
Proteinortho 4.26 [134] Biology, Genomics
python 2.6.8, 2.7.3 [135] Programming, scripting, language
QIIME 1.5.0 [136] Biology, Ecology
R 2.15.1, 2.15.0-mpi, Rmpi/2.15.1, 3.0.0 [137] Statistics, Programming
R8S 1.71 [138] Biology, Evolution
RADICAL 0.2 [139] Biology, Phylogenetics, Genomics
RAxML 7.3.2.0705 [140] Biology, Phylogenetics
RepeatMasker 3.3.0 [141] Biology, Genomics
Reptile 1.1 [142] Biology, NGS, error correction
riboPicker 0.4.3 [143] Biology, Sequence
RSEG 0.4.8 [144] Biology, NGS
samtools 0.1.16, 0.1.18, 0.1.19 [145] Biology, NGS
SAS 9.3 [146] Statistics, Graphing
SATe 2.2.7 [147] Biology, Phylogenetics
Schrodinger 2012 [148] Simulation, chemistry
SeqPrep 0.5 [149] Biology, NGS
SEQuel 1.0.1 [150] Biology, NGS
Sickle 1.200 [151] Biology, NGS, quality filter
Siesta 2.0.2,3.1 [152] Simulation, Physics, Ab Initio
SIFT 4.0.3b [153] Biology, Genomics
Silo 4.7 [154] Library, Data
Snap 20100728 [155] Biology, Genomics
SOAPdenovo 1.05 [156] Biology, NGS
SOAPdenovo-Trans 1.01 [157] Biology, NGS
SPARTA+ 2.60 [158] Chemistry
SPIMAP 1.1 [159] Biology, Phylogenetics
SpliceTrap 0.90.5 [160] Biology, NGS, RNA-Seq
Sputnik 1.0 [161] Biology, Genomics
SRA 2.1.10 [162]] biology, NGS
SSPACE 2.0 [163] Biology, NGS
Stacks 0.9995 [164] Biology, Genomics, NGS
Structure 2.3.3 [165] Biology, Population
Swig 2.0.9 [166] Programming, C, C++, Python
TAU 2.21.4 [167] Profiling, Tracing, Programming
tgicl 2.1 [168] Biology, sequencing, clustering
Tophat 1.4.1, 2.0.1 [169] Biology, NGS
TreeFix 1.1.7 [170] Biology, Phylogenetics
TRF 4.04 [171] Biology, Genomics
Trimmomatic 0.22 [172] Biology, NGS
Trinity r20120905, r20121005, r20120225 [173] Biology, RNA-Seq
Twinscan 4.1.2 [174] Biology, Genomics
usearch 5.2.32 [175] Biology, Sequence analysis
VASP 4.6.34, 5.2.12, 5.3.2 [176] Quantum Chemistry, Ab Initio
VCFtools 0.1.9, 0.1.10 [177] Biology, SNPs
velvet 1.2.06, 1.2.07 [178] Biology, NGS
vmd 1.9.1 [179] Biology, Visualization
WebLogo 3.3 [180] Biology, Genomics
WDSSII 1 [181] Meteorology
WIEN2k 12.1 [182] Material Science, Chemistry
wgs 7.0.1.22 [183] Biology, NGS
wublast 2.0 [184] Biology, Sequence Alignment
Yasra 2.32 [185] Biology, NGS
  1. ↑ Up to 3 most recent/important releases are listed. See the software wiki pages and the output of "module spider software" for full version listing.

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

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