Difference between revisions of "Installed Software"

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| [[Bbcp]] || 12.08.17.00.0  || [http://www.slac.stanford.edu/~abh/bbcp/]|| Network file transfer
 
| [[Bbcp]] || 12.08.17.00.0  || [http://www.slac.stanford.edu/~abh/bbcp/]|| Network file transfer
 
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|-
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| [[Bcftools]] || 20140618 || [http://samtools.github.io/bcftools/]] || Biology, Genomics, NGS
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| [[Bcftools]] || 20140618 || [http://samtools.github.io/bcftools/] || Biology, Genomics, NGS
 
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|-
 
| [[Beagle|BEAGLE]] || 3.2.2 || [http://faculty.washington.edu/browning/beagle/beagle.html] || Biology, Genetics, Genotyping  
 
| [[Beagle|BEAGLE]] || 3.2.2 || [http://faculty.washington.edu/browning/beagle/beagle.html] || Biology, Genetics, Genotyping  

Revision as of 13:33, 29 August 2014

Installed Software List

Last updated 2014-08-29.

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 1.3.4, 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
BPP 2.2, 1.9.0 [39] Biology, Phylogenetics
BRANCH 1.8.1 [40] Biology, NGS, Mapping
Bwa 0.6.1, 0.7.9a, 0.7.10 [41] Biology, NGS
Camino 20140723 [42] Biology, Neuroscience, Imaging
CAP3 20120705 [43] Biology, sequence assembly
CASAVA 1.8.2 [44] Biology, NGS
CD-HIT 4.6 [45] Biology, Genomics
CDO 1.6.1 [46] Climate
CEAS 1.0.2 [47] Biology, Genomics
CellProfiler 2.0 [48] Biology, Image Analysis
Charmm 36a3 [49] Simulation, Chemistry
Chartdirector 5.1.0 [50] Graphics
Chimera 1.7 [51] Biology, Modeling
CIMS 4.1.2 [52] Biology, Genomics
Circos 0.63-pre11 [53] Biology, Visualization
CisGenome 2.0 [54] Biology, Genomics, Peak Calling
CLHEP 2.2.0.1 [55] High Energy Physics
ClonalFrame 1.1, 1.2 [56] Biology, Genomics, NGS
ClustalW 2.1 [57] Biology, Genomics
Clview 20130402 [58] Biology, Genomics
CMake 2.8.8 [59] Programming, Build System
CNVSeq 20110715 [60] Biology, NGS
Coevol 1.3c, 1.4b [61] Biology, Phylogenetics
CoMap 1.4.1 [62] Biology, Genomics
CONCOCT 0.3.1 [63] Biology, Genomics
Consed 23.0 [64] Biology, Genomics
covNMR 2014 [65] Biochemistry
CUDA 4.2, 5.5 [66] Programming, Graphics
Cufflinks 1.3.0, 2.0.2, 2.2.1 [67] Biology, NGS
Cutadapt 1.1 [68] Biology, NGS
DAKOTA 5.4.0 [69] Computational Science
DCMTK 3.6.0 [70] Biology, Neuroscience, Imaging
DDSCAT 7.3.0 [71] Astrophysics
DDT 4.1.0, 4.2.1 [72] Software
Delft3D 3621 [73] Hydrodynamics, Physics
Desmond 3.0.3.1 [74] Simulation, Biology, Chemistry
Dalton 2011 [75] Quantum Chemistry
DiffReps 1.55.4 [76] Biology, NGS, ChIP-Seq
Dindel 1.01 [77] Biology, NGS
DIYABC 1.0.4.43b, 2.0.3 [78] Biology, Genomics
Dlpoly 4.03.4 [79] Simulation, Biology, Chemistry
DNA Clust 3.0 [80] Biology, Genomics
Dock 6.5, 6.6 [81] Chemistry, ligand binding prediction
DOT 2.0 [82] Biology, Bioinformatics, Docking
Doxygen 1.8.3.1 [83] Programming, Documentation
DSSP 2.2.1 [84] Biology, Molecular Dynamics
DTI-TK 2.3.1 [85] Biology, Neurology, Imaging
EA-Utils 1.1.2.537 [86] Biology, NGS
ECTools 20140311 [87] Biology, Sequencing, Bioinformatics
EEGLAB 12.0.2.1b [88] Biology, Matlab
EIGENSOFT 4.2, 5.0.1 [89] Biology, Population
emboss 6.5.7 [90] Biology, multi-tool suite
EMIRGE 20130727 [91] Biology, NGS
eQTLA 1.1 [92] Biology, Genomics
Eqtlbma 1.2.2 [93] Biology, Genotyping
Espresso 5.0.1 [94] Modeling, Physics
ESPRIT 201211 [95] Biology, NGS, Metagenomics
ETE2 2.1 [96] Biology, Phylogenetics
Eval 2.2.8 [97] Biology, Genomics, GUI
ExaML 1.0.3, 1.0.5, 1.0.12 [98] Biology, Phylogenetics
Exonerate 2.2.0 [99] Biology, Genomics
eXpress 1.3.1 [100] Biology, NGS
FAR 2.15 [101] Biology, Genomics
FASTA 34.26.5, 36.3.6d [102] Biology, Genomics
FastML 3.0 [103] Biology, Phylogenetics, ML
FastQC 0.9.6, 0.10.1 [104] Biology, NGS
FastTree 2.1.7 [105] Biology, Phylogenetics
Fastx_toolkit 0.0.13.2 [106] Biology, NGS
fcGENE 1.0.7 [107] Biology, Genomics, SNP
Ferret 6.82 [108] Oceanography, Meteorology
FFmpeg 2.1.3 [109] Multimedia, audio, video
FFTW 3.3.2, 3.3.3 [110] Math, Library, C++
FLASH 1.2.10 [111] Biology, Genomics, NGS
Flexbar 2.3 [112] Biology, Genomics, NGS
Fluent 14.5.7, 15.0 [113] Simulation, Fluid Dynamics
FragGeneScan 1.16 [114] Biology, NGS, Genomics
FreeBayes 0.9.6, 0.9.15 [115] Biology, NGS, SNP Calling
Freesurfer 5.2.0 [116] Biology, Neurology, Imaging
FSL 5.0.2.2 [117] Biology, Neurology, Imaging
Garli 2.0, 2.01 [118] Biology, Phylogenetics
GASVPro 201310 [119] Biology, NGS, Genomics
GATE 7.0 [120] Data Analysis
GATK 1.6.9, 2.7.4, 3.1.1 [121] Biology, NGS
Gaussian E01, G03, G09-A.02, G09-C.01 [122] Modeling, Computational Chemistry
Geant4 4.10 [123] Physics
GEM 20130406 [124] Biology, NGS
GEMINI 4.6.6a [125] Biology, Genomics, Genetics
GenBank Tools 20140130 [126] BIology< Genomics
GeneMark 2012.04 [127] Biology, Genomics, Metagenomics
Genewise 2.2.0 [128] Biology, Genomics, Annotation
GenomicTools 2.7.0 [129] Biology, NGS
Git 1.8.2.1 [130] Development, Revision Control
Gmap 20130618, 20130720, 20140530 [131] Biology, Genomics
GnuPlot 4.6.0 [132] Graphics, Plotting, Programming
Grace 5.1.22 [133] Graphics, plotting, 2D
GrADS 2.0.1 [134] Earth Science
GraphViz 2.38.0 [135] Graphics, plotting, visualization
Gromacs 4.5.5, 4.6.5 [136] Chemistry, Modeling, Simulation
GSNP 1.0 [137] Biology, Bioinformatics, NGS
GSL 1.15 [138] Library, Math, C++, C
GULP 4.0 [139] Material Science
HaMStR v8b [140] Biology, Genomics
Hapsembler 2.21 [141] Biology, Genomics, NGS
HDF5 1.8.9, 1.8.12 [142] Library, Data
HMMER3 3.0 [143] Biology, Genomics
HMMSplicer 0.9.5 [144] Biology, Genomics
HOMER 4.2 [145] Biology, Genomics
HTSeq 0.5.3p3, 0.6.1p1 [146] Biology, NGS
HyPhy 2.1.2.28 [147] Biology, Phylogenetics
Hypre 1.10.0b, 2.8.0b [148] Library, Math, Physics
IDBA-UD 1.0.9, 1.1.0 [149] Biology, NGS
iGTP 1.1 [150] Biology, Bioinformatics, Phylogenetics
IM and IMa 20091217 [151] Biology, Population
IMa2 20120827 [152] Biology, Population
ImageMagick 6.8.8-9 [153] Image manipulation
Intel Compilers 11.1, 2012 [154] Programming, Compilers
IOAPI 3.1 [155] Meteorology
Iprscan 4.8 [156] Biology, Genomics
ITK 4.3.1 [157] Biology, Genomics
ITK-SNAP 3.0.0 [158] Biology, Neuroscience, Imaging
JAGS 3.3.0 [159] Statistics
Java 1.6.0_31, 1.7.0_02 [160] Java Development Kit
Kent 20120524 [161] Biology, NGS
Khmer 1.1 [162] Biology, NGS
Kmer 1934 [163] Biology, NGS
KmerGenie 1.6741 [164] Biology, NGS, Utilities
LAMMPS 28Oct12, 30Sep13 [165] Molecular Dynamics Simulation
Last 193, 247 [166] Biology, Sequence alignment
Lastz 1.03.02, 1.02.00 [167] Biology, NGS
LIBSVM 3.12 [168] Machine Learning
LSC 0.3, 0.3.1 [169] Biology, NGS, Error correction
Loci 3.3 [170] Fluid Dynamics
LS-DYNA 700, 711 [171] Physics
MACH 1.0.18 [172] Biology, Genomics
MACS 1.4.2 [173] Biology, ChIP-Seq
mafft 7.037, 6.903 [174] Biology, Multiple sequence alignment
Maker 2.10, 2.25b [175] Biology, Annotation, Genomics
Maq 0.7.1 [176] Biology, NGS
Matlab 2012a, 2013a, 2014a [177] Math, Simulation, Programming
MATS 2.1.0, 3.0.6b, 3.0.8 [178] BIology, NGS
MCarts 1.0.2 [179] Biology, Genomics, Markov models
MCNP 5, 6b2 [180] Physics
MCNPX 2.7.0, 2.7.0-i8 [181] Physics
Meme 4.8.1 [182] Biology, Motifs, Sequence analysis
Mercurial 2.7 [183] Development, Revision Control
Metabin 1.0 [184] Biology, Metagenomics
MetaCluster 5.0beta [185] Biology, Metagenomics
MetaCV 2.3.0 [186] Biology, NGS
MetaVelvet 1.2.01 [187] Biology, NGS
MetaGeneMark 2012.04 [188] Biology, Genomics
Mfold 3.6 [189] Biology, Genomics
Midnight Commander 4.6.1 [190] Tools, Utilities
Migrate-n 3.3.0 [191] Biology, Population
mira 3.2.0, 3.4.0.1, 3.9.9, 3.9.18, 4.0.rc1 [192] Biology, NGS
MISO 0.4.4, 0.4.9 [193] Biology, NGS
MSMBuilder 2.5.1 [194] Molecular Dynamics
Modeller 9.11, 9.13, 9.14 [195] Biology, Modeling
Molden 5.0 [196] Molecular, electronic structure
mosaik 2.1.33 [197] Biology,NGS
Mothur 1.31.2 [198] Biology, Microbial Ecology
MP-EST 1.4 [199] Biology, Phylogenetics
mpiP 3.4.1 [200] Parallel Computing
MrBayes 3.2.1 [201] Biology, Phylogenetics
MRIcron 201306 [202] Biology, MRI, Imaging
MUMmer 3.23 [203] Biology, Genomics
MUSCLE 3.8.31 [204] Biology, Genomics
NAMD 2.9 [205] Simulation, Chemistry, Biology
Nbody 6 [206] Astronomy
NCBI C++ Toolkit 12.0.0 [207] Biology, C++, Development
NCL 6.1.2 [208] Atmosphere Science
NCO 4.2.1, 4.4.3 [209] Data exchange tools
Ncview 2.1.2 [210] Data visualization
NetCDF 3.4.2, 4.2, 4.3 [211] Data exchange, Tools
Newbler 2.6, 2.7 [212] Biology, NGS
Nexus NCL 2.1.18 [213] Biology, Phylogenetics, Library
NMRPipe 7.9 [214] Biology, Biochemistry
Novoalign 2.08.02, 3.00.02 [215] Biology, NGS
Oases 0.2.08 [216] Biology, NGS
Olego 1.1.2, 1.1.5 [217] Biology, NGS, RNA-Seq
Octave 3.6.4 [218] Numerical Computation
OpenBabel 2.3.2 [219] Biology, Chemistry
OpenCV 2.4.8 [220] Computervision
OpenFOAM 2.1.1 [221] Fluid Dynamics
OrthoMCL 2.0.2, 2.0.3, 2.0.7 [222] Biology, Genomics
PAML 4.7 [223] Biology, Phylogenetics
ParaView 4.1.0 [224] Data Analysis
PartitionFinder 1.0.1, 1.1.1 [225] Biology, Phylogenetics, Evolution
Parflow v615 [226] Ecology, Modeling
PASA 1.5, 2.0-r20130605p1, 2.0-r20130907 [227] Biology, Genomics
PBJelly 14.7.14 [228] Biology, Bioinformatics
PeakSplitter 1.0 [229] Biology, Chip-Seq
PDT 3.18 [230] Programming, Profiler
Perl 5.16.0 [231] Programming, Language
PerM 0.4.0 [232] Biology, NGS
PETSc 2.3, 3.3 [233] Math, Numerical solvers
Phenix 1.8.1069 [234] Crystallography
PHITS 2.52 [235] Physics
PhyloBayes 3.3f, 1.4f MPI [236] Biology, Phylogenetics
PhyML 3.0, 20121109 [237] Biology, Phylogenetics
Picard 1.69, 1.72, 1.80 [238] Biology, NGS
Preseq 0.0.4 [239] Biology, NGS
ProBABEL 0.4.2 [240] Biology, Genomics, GWAS
Proovread 1.03rcl [241] Biology, Genomics, NGS
Proteinortho 4.26 [242] Biology, Genomics
python 2.6.8, 2.7.3 [243] Programming, scripting, language
QIIME 1.5.0 [244] Biology, Ecology
QT 4.8.3 [245] Computer Science
Quickquartet 1.0.0 [246] Biology, Phylogenetics
R 2.15.1, 2.15.0-mpi, Rmpi/2.15.1, 3.0.0 [247] Statistics, Programming
R8S 1.71 [248] Biology, Evolution
RADICAL 0.2 [249] Biology, Phylogenetics, Genomics
RAxML 7.9.1, 8.0.0, 8.0.25 [250] Biology, Phylogenetics
RepeatMasker 3.3.0 [251] Biology, Genomics
Reptile 1.1 [252] Biology, NGS, error correction
riboPicker 0.4.3 [253] Biology, Sequence
RNAhybrid 2.1.1 [254] Biology, Genomics
ROOT 6.0 [255] Data Analysis
RSEG 0.4.8 [256] Biology, NGS
Sailfish 0.6.3 [257] Biology, NGS, RNA-Seq
samtools 0.1.16, 0.1.18, 0.1.19 [258] Biology, NGS
SAS 9.3 [259] Statistics, Graphing
SATe 2.2.7 [260] Biology, Phylogenetics
Sharcgs 1.2.11 [261] Biology, NGS, de novo assembly
Schrodinger 2012, 2013 [262] Simulation, chemistry
SeqPrep 0.5 [263] Biology, NGS
SEQuel 1.0.1 [264] Biology, NGS
Seqtk 20140729 [265] Biology, NGS
SeqyClean 1.8.10 [266] Biology, NGS, quality filter
Sickle 1.200 [267] Biology, NGS, quality filter
Siesta 2.0.2,3.1 [268] Simulation, Physics, Ab Initio
SIFT 4.0.3b [269] Biology, Genomics
Silo 4.7 [270] Library, Data
Slicer 4.3.1 [271] Biology, Imaging
SMALT 0.7.6 [272] Biology, NGS
Snap 20100728 [273] Biology, Genomics
SOAPdenovo 1.05 [274] Biology, NGS
SOAPdenovo-Trans 1.01, 1.03 [275] Biology, NGS
SparCC 201402 [276] Microbial Ecology
Spades 2.5.0, 2.5.1, 3.0.0 [277] Biology, NGS
Spanki 0.4.1, 0.4.3 [278] Biology, NGS, RNA-Seq
SPARTA+ 2.60 [279] Chemistry
SPIMAP 1.1 [280] Biology, Phylogenetics
SpliceTrap 0.90.5 [281] Biology, NGS, RNA-Seq
SPM 8 [282] Biology, Statistics, Neurology, Imaging
Sputnik 1.0 [283] Biology, Genomics
SRA 2.1.10 [284]] biology, NGS
SSPACE 2.0 [285] Biology, NGS
Stacks 0.9995 [286] Biology, Genomics, NGS
STAR 2.3.0e [287] Biology, NGS, Alignment
STAR-CCM+ 8.06 [288] Mechanical Engineering
Stata 10.1, 13 [289] Statistics, Data analysis
Stringtie 0.97 [290] Biology, NGS, Alignment
Structure 2.3.3, 2.3.4 [291] Biology, Population
SUNDIALS 2.3.0, 2.5.0 [292] Numerical Solver
swak4Foam 2.x [293] Fluid Dynamics
swarm 1.2.11 [294] Data Analysis
Swig 2.0.9 [295] Programming, C, C++, Python
Syzygy 1.2.7 [296] Biology, Genomics
TASSEL 5.0 [297] Biology, Genomics
TAU 2.21.4, 2.23 [298] Profiling, Tracing, Programming
T-Coffee 9.03.r1318 [299] Biology, Genomics, Multiple Alignment
TESS 2.3.1 [300] Biology, Genomics, Markov
tgicl 2.1 [301] Biology, sequencing, clustering
Tophat 1.4.1, 2.0.1, 2.0.8b [302] Biology, NGS
Totalview 8.12.0 [303] Computer Science
TPP 4.7.0 [304] Bioinformatics, MassSpec
TreeFix 1.1.7 [305] Biology, Phylogenetics
TRF 4.04 [306] Biology, Genomics
Trilinos 11.4.1, 11.8.1 [307] Math Algorithm
Trimmomatic 0.22, 0.32 [308] Biology, NGS
Trinity r20131110, r20140413 [309] Biology, NGS, RNA-Seq
Twinscan 4.1.2 [310] Biology, Genomics
usearch 5.2.32, 7.0.959, 7.0.1001-64 (licensed 64-bit) [311] Biology, Sequence analysis
Valgrind 3.9.0 [312] Computer Science
VASP 4.6.34, 5.2.12, 5.3.2, 5.3.3, 5.3.5 [313] Quantum Chemistry, Ab Initio
VCFtools 0.1.9, 0.1.10 [314] Biology, SNPs
velvet 1.2.06, 1.2.07, 1.2.10 [315] Biology, NGS
vmd 1.9.1 [316] Biology, Visualization
Wannier90 1.2, 2.0.0 [317] Computational Physics
WebLogo 3.3 [318] Biology, Genomics
WDSSII 1 [319] Meteorology
WIEN2k 12.1 [320] Material Science, Chemistry
wgs 7.0.1.22 [321] Biology, NGS
wublast 2.0 [322] Biology, Sequence Alignment
Yambo 3.3.0 [323] Physics
Yasra 2.32 [324] 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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