Difference between revisions of "Installed Software"

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Revision as of 22:12, 17 June 2014

Installed Software List

Last updated 2014-06-17.

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
Amuse 6.0 [8] Astrophysics
Affymetrix Power Tools 1.15.0 [9] Biology, Genomics, Microarray
AtomEye 3 [10] Material Science
Augustus 2.6 [11] Biology, NGS
BamBam 1.0 [12] Biology, NGS
Bamstats 20140602 [13] Biology, NGS
Bamtools 2.1.1 [14] Biology, NGS
BamUtil 1.0.2 [15] Biology, NGS
BayesRate 1.3.43 [16] Biology, Phylogenetics
Bbcp 12.08.17.00.0 [17] Network file transfer
BEAGLE 3.2.2 [18] Biology, Genetics, Genotyping
BEAST 1.7.5, 2.0.1, 2.0.2.pre [19] Biology, Phylogenetics
BEDTools 2.16.2, 2.17.0 [20] Biology, NGS
BEST 2.3 [21] Biology, Phylogenetics
BETA 1.0.5 [22] Biology, NGS
BFAST 0.7.0 [23] Biology, NGS
Bismark 0.7.4, 0.7.7 [24] Biology, Methylation, NGS
Bioconductor Latest [25] Biology, R, Statistics
BioPerl 1.006901 [26] Biology, Perl
BioPython 1.59 [27] Biology, Python
BLASR 20130815 [28] Biology, NGS
NCBI BLAST 2.2.27, 2.2.28, 2.2.29 [29] Biology, Sequence alignment
Blast2go 2.5.0-20120705 [30] Biology, Annotation
BLAT 20120524 [31] Biology, Sequence alignment
Boost 1.49.0, 1.53.0, 1.54.0 [32] C++, Library
Bwa 0.6.1, 0.7.8, 0.7.9a [33] Biology, NGS
Bowtie 0.12.8, 0.12.9, 1.0.0 [34] Biology, NGS
Bowtie2 2.1.0, 2.2.2, 2.2.3 [35] Biology, NGS
CAP3 20120705 [36] Biology, sequence assembly
CASAVA 1.8.2 [37] Biology, NGS
CD-HIT 4.6 [38] Biology, Genomics
CDO 1.6.1 [39] Climate
CEAS 1.0.2 [40] Biology, Genomics
CellProfiler 2.0 [41] Biology, Image Analysis
Charmm 36a3 [42] Simulation, Chemistry
Circos 0.63-pre11 [43] Biology, Visualization
CisGenome 2.0 [44] Biology, Genomics, Peak Calling
ClustalW 2.1 [45] Biology, Genomics
Clview 20130402 [46] Biology, Genomics
CMake 2.8.8 [47] Programming, Build System
CoMap 1.4.1 [48] Biology, Genomics
CONCOCT 0.3.1 [49] Biology, Genomics
Consed 23.0 [50] Biology, Genomics
covNMR 2014 [51] Biochemistry
CUDA 4.2, 5.5 [52] Programming, Graphics
Cufflinks 1.3.0, 2.1.1, 2.2.0 [53] Biology, NGS
Cutadapt 1.1 [54] Biology, NGS
DAKOTA 5.4.0 [55] Computational Science
DDSCAT 7.3.0 [56] Astrophysics
Delft3D 3621 [57] Hydrodynamics, Physics
Desmond 3.0.3.1 [58] Simulation, Biology, Chemistry
Dalton 2011 [59] Quantum Chemistry
DiffReps 1.55.4 [60] Biology, NGS, ChIP-Seq
Dindel 1.01 [61] Biology, NGS
DIYABC many [62] Biology, Genomics
Dlpoly 4.03.4 [63] Simulation, Biology, Chemistry
DNA Clust 3.0 [64] Biology, Genomics
Dock 6.5, 6.6 [65] Chemistry, ligand binding prediction
DSSP 2.2.1 [66] Biology, Molecular Dynamics
DTI-TK 2.3.1 [67] Biology, Neurology, Imaging
EA-Utils 1.1.2.537 [68] Biology, NGS
EIGENSOFT 4.2, 5.0.1 [69] Biology, Population
emboss 6.5.7 [70] Biology, multi-tool suite
eQTLA 1.1 [71] Biology, Genomics
Espresso 5.0.1 [72] Modeling, Physics
ESPRIT 201211 [73] Biology, NGS, Metagenomics
ETE2 2.1 [74] Biology, Phylogenetics
Eval 2.2.8 [75] Biology, Genomics, GUI
ExaML 1.0.3, 1.0.5, 1.0.12 [76] Biology, Phylogenetics
Exonerate 2.2.0 [77] Biology, Genomics
FAR 2.15 [78] Biology, Genomics
FASTA 34.26.5, 36.3.6d [79] Biology, Genomics
FastML 3.0 [80] Biology, Phylogenetics, ML
FastQC 0.9.6, 0.10.1 [81] Biology, NGS
FastTree 2.1.7 [82] Biology, Phylogenetics
Fastx_toolkit 0.0.13.2 [83] Biology, NGS
fcGENE 1.0.7 [84] Biology, Genomics, SNP
Ferret 6.82 [85] Oceanography, Meteorology
FFmpeg 2.1.3 [86] Multimedia, audio, video
FFTW 3.3.2, 3.3.3 [87] Math, Library, C++
FLASH 1.2.10 [88] Biology, Genomics, NGS
Fluent 14.5.7, 15.0 [89] Simulation, Fluid Dynamics
FragGeneScan 1.16 [90] Biology, NGS, Genomics
FreeBayes 0.9.6 [91] Biology, NGS, SNP Calling
Freesurfer 5.2.0 [92] Biology, Neurology, Imaging
FSL 5.0.2.2 [93] Biology, Neurology, Imaging
Garli 2.0, 2.01 [94] Biology, Phylogenetics
GASVPro 201310 [95] Biology, NGS, Genomics
GATK 1.6.9, 2.7.4, 3.1.1 [96] Biology, NGS
Gaussian E01, G03, G09-A.02, G09-C.01 [97] Modeling, Computational Chemistry
GEMINI 4.6.6a [98] Biology, Genomics, Genetics
GenBank Tools 20140130 [99] BIology< Genomics
GeneMark 2012.04 [100] Biology, Genomics, Metagenomics
Genewise 2.2.0 [101] Biology, Genomics, Annotation
GenomicTools 2.7.0 [102] Biology, NGS
Git 1.8.2.1 [103] Development, Revision Control
Gmap 20130618, 20130720, 20140530 [104] Biology, Genomics
GnuPlot 4.6.0 [105] Graphics, Plotting, Programming
Grace 5.1.22 [106] Graphics, plotting, 2D
GrADS 2.0.1 [107] Earth Science
Gromacs 4.5.5, 4.6.5 [108] Chemistry, Modeling, Simulation
GSL 1.15 [109] Library, Math, C++, C
GULP 4.0 [110] Material Science
HaMStR v8b [111] Biology, Genomics
HDF5 1.8.9, 1.8.12 [112] Library, Data
HMMER3 3.0 [113] Biology, Genomics
HMMSplicer 0.9.5 [114] Biology, Genomics
HOMER 4.2 [115] Biology, Genomics
HTSeq 0.5.3p3, 0.6.1p1 [116] Biology, NGS
HyPhy 2.1.2.28 [117] Biology, Phylogenetics
Hypre 1.10.0b, 2.8.0b [118] Library, Math, Physics
IDBA-UD 1.0.9, 1.1.0 [119] Biology, NGS
IM and IMa 20091217 [120] Biology, Population
IMa2 20120827 [121] Biology, Population
ImageMagick 6.8.8-9 [122] Image manipulation
Intel Compilers 11.1, 2012 [123] Programming, Compilers
IOAPI 3.1 [124] Meteorology
Iprscan 4.8 [125] Biology, Genomics
ITK 4.3.1 [126] Biology, Genomics
JAGS 3.3.0 [127] Statistics
Java 1.6.0_31, 1.7.0_02 [128] Java Development Kit
Kent 20120524 [129] Biology, NGS
Kmer 1934 [130] Biology, NGS
LAMMPS 28Oct12, 30Sep13 [131] Molecular Dynamics Simulation
Last 193, 247 [132] Biology, Sequence alignment
Lastz 1.03.02, 1.02.00 [133] Biology, NGS
LIBSVM 3.12 [134] Machine Learning
LSC 0.3, 0.3.1 [135] Biology, NGS, Error correction
Loci 3.3 [136] Fluid Dynamics
LS-DYNA 700, 711 [137] Physics
MACH 1.0.18 [138] Biology, Genomics
MACS 1.4.2 [139] Biology, ChIP-Seq
mafft 7.037, 6.903 [140] Biology, Multiple sequence alignment
Maker 2.10, 2.25b [141] Biology, Annotation, Genomics
Maq 0.7.1 [142] Biology, NGS
Matlab 2012a, 2013a, 2014a [143] Math, Simulation, Programming
MATS 2.1.0, 3.0.6b, 3.0.8 [144] BIology, NGS
Mauve 2.3.1 [145] Biology, Genomics, Multiple genome alignments
MCNP 5, 6b2 [146] Physics
MCNPX 2.7.0, 2.7.0-i8 [147] Physics
Meme 4.8.1 [148] Biology, Motifs, Sequence analysis
Mercurial 2.7 [149] Development, Revision Control
Metabin 1.0 [150] Biology, Metagenomics
MetaCluster 5.0beta [151] Biology, Metagenomics
MetaVelvet 1.2.01 [152] Biology, NGS
MetaGeneMark 2012.04 [153] Biology, Genomics
Mfold 3.6 [154] Biology, Genomics
Midnight Commander 4.6.1 [155] Tools, Utilities
Migrate-n 3.3.0 [156] Biology, Population
mira 3.2.0, 3.4.0.1, 3.9.9, 3.9.18, 4.0.rc1 [157] Biology, NGS
MISO 0.4.4, 0.4.9 [158] Biology, NGS
MSMBuilder 2.5.1 [159] Molecular Dynamics
Molden 5.0 [160] Molecular, electronic structure
mosaik 2.1.33 [161] Biology,NGS
Mothur 1.31.2 [162] Biology, Microbial Ecology
mpiP 3.4.1 [163] Parallel Computing
MrBayes 3.2.1 [164] Biology, Phylogenetics
MUMmer 3.23 [165] Biology, Genomics
MUSCLE 3.8.31 [166] Biology, Genomics
NAMD 2.9 [167] Simulation, Chemistry, Biology
Nbody 6 [168] Astronomy
NCBI C++ Toolkit 12.0.0 [169] Biology, C++, Development
NCL 6.1.2 [170] Atmosphere Science
NCO 4.2.1, 4.4.3 [171] Data exchange tools
NetCDF 4.2 [172] Data exchange, Tools
Newbler 2.6, 2.7 [173] Biology, NGS
Nexus NCL 2.1.18 [174] Biology, Phylogenetics, Library
NMRPipe 7.9 [175] Biology, Biochemistry
Novoalign 2.08.02, 3.00.02 [176] Biology, NGS
Oases 0.2.08 [177] Biology, NGS
Olego 1.1.2 [178] Biology, NGS, RNA-Seq
Octave 3.6.4 [179] Numerical Computation
OpenBabel 2.3.2 [180] Biology, Chemistry
OpenCV 2.4.8 [181] Computervision
OpenFOAM 2.1.1 [182] Fluid Dynamics
OrthoMCL 2.0.2, 2.0.3, 2.0.7 [183] Biology, Genomics
PAML 4.7 [184] Biology, Phylogenetics
PartitionFinder 1.0.1 [185] Biology, Phylogenetics, Evolution
Parflow v615 [186] Ecology, Modeling
PASA 1.5, 2.0-r20130605p1, 2.0-r20130907 [187] Biology, Genomics
PeakSplitter 1.0 [188] Biology, Chip-Seq
PDT 3.18 [189] Programming, Profiler
Perl 5.16.0 [190] Programming, Language
PerM 0.4.0 [191] Biology, NGS
PETSc 2.3, 3.3 [192] Math, Numerical solvers
Phenix 1.8.1069 [193] Crystallography
PHITS 2.52 [194] Physics
PhyloBayes 3.3f, 1.4f MPI [195] Biology, Phylogenetics
PhyML 3.0, 20121109 [196] Biology, Phylogenetics
Picard 1.69, 1.72, 1.80 [197] Biology, NGS
Preseq 0.0.4 [198] Biology, NGS
ProBABEL 0.4.2 [199] Biology, Genomics, GWAS
Proteinortho 4.26 [200] Biology, Genomics
python 2.6.8, 2.7.3 [201] Programming, scripting, language
QIIME 1.5.0 [202] Biology, Ecology
QT 4.8.3 [203] Computer Science
Quickquartet 1.0.0 [204] Biology, Phylogenetics
R 2.15.1, 2.15.0-mpi, Rmpi/2.15.1, 3.0.0 [205] Statistics, Programming
R8S 1.71 [206] Biology, Evolution
RADICAL 0.2 [207] Biology, Phylogenetics, Genomics
RAxML 7.9.1, 8.0.0, 8.0.25 [208] Biology, Phylogenetics
RepeatMasker 3.3.0 [209] Biology, Genomics
Reptile 1.1 [210] Biology, NGS, error correction
riboPicker 0.4.3 [211] Biology, Sequence
RNAhybrid 2.1.1 [212] Biology, Genomics
RSEG 0.4.8 [213] Biology, NGS
Sailfish 0.6.3 [214] Biology, NGS, RNA-Seq
samtools 0.1.16, 0.1.18, 0.1.19 [215] Biology, NGS
SAS 9.3 [216] Statistics, Graphing
SATe 2.2.7 [217] Biology, Phylogenetics
Sharcgs 1.2.11 [218] Biology, NGS, de novo assembly
Schrodinger 2012, 2013 [219] Simulation, chemistry
SCons 2.3.0 [220] Programming, Build System
SeqPrep 0.5 [221] Biology, NGS
SEQuel 1.0.1 [222] Biology, NGS
SeqyClean 1.8.10 [223] Biology, NGS, quality filter
Sickle 1.200 [224] Biology, NGS, quality filter
Siesta 2.0.2,3.1 [225] Simulation, Physics, Ab Initio
SIFT 4.0.3b [226] Biology, Genomics
Silo 4.7 [227] Library, Data
Snap 20100728 [228] Biology, Genomics
SOAPdenovo 1.05 [229] Biology, NGS
SOAPdenovo-Trans 1.01, 1.03 [230] Biology, NGS
SparCC 201402 [231] Microbial Ecology
Spades 2.5.0, 2.5.1, 3.0.0 [232] Biology, NGS
Spanki 0.4.1, 0.4.3 [233] Biology, NGS, RNA-Seq
SPARTA+ 2.60 [234] Chemistry
SPIMAP 1.1 [235] Biology, Phylogenetics
SpliceTrap 0.90.5 [236] Biology, NGS, RNA-Seq
SPM 8 [237] Biology, Statistics, Neurology, Imaging
Sputnik 1.0 [238] Biology, Genomics
SRA 2.1.10 [239]] biology, NGS
SSPACE 2.0 [240] Biology, NGS
Stacks 0.9995 [241] Biology, Genomics, NGS
STAR-CCM+ 8.06 [242] Mechanical Engineering
Stata 10.1, 13 [243] Statistics, Data analysis
Structure 2.3.3, 2.3.4 [244] Biology, Population
SUNDIALS 2.3.0, 2.5.0 [245] Numerical Solver
swak4Foam 2.x [246] Fluid Dynamics
Swig 2.0.9 [247] Programming, C, C++, Python
TAU 2.21.4, 2.23 [248] Profiling, Tracing, Programming
T-Coffee 9.03.r1318 [249] Biology, Genomics, Multiple Alignment
tgicl 2.1 [250] Biology, sequencing, clustering
Tophat 1.4.1, 2.0.1, 2.0.8b [251] Biology, NGS
Totalview 8.12.0 [252] Computer Science
TPP 4.7.0 [253] Bioinformatics, MassSpec
TreeFix 1.1.7 [254] Biology, Phylogenetics
TRF 4.04 [255] Biology, Genomics
Trilinos 11.4.1, 11.8.1 [256] Math Algorithm
Trimmomatic 0.22 [257] Biology, NGS
Trinity r20131110, r20140413 [258] Biology, NGS, RNA-Seq
Twinscan 4.1.2 [259] Biology, Genomics
usearch 5.2.32, 7.0.959, 7.0.1001-64 (licensed 64-bit) [260] Biology, Sequence analysis
Valgrind 3.9.0 [261] Computer Science
VASP 4.6.34, 5.2.12, 5.3.2, 5.3.3 [262] Quantum Chemistry, Ab Initio
VCFtools 0.1.9, 0.1.10 [263] Biology, SNPs
velvet 1.2.06, 1.2.07, 1.2.10 [264] Biology, NGS
vmd 1.9.1 [265] Biology, Visualization
Wannier90 2.0.0 [266] Computational Physics
WebLogo 3.3 [267] Biology, Genomics
WDSSII 1 [268] Meteorology
WIEN2k 12.1 [269] Material Science, Chemistry
wgs 7.0.1.22 [270] Biology, NGS
wublast 2.0 [271] Biology, Sequence Alignment
Yambo 3.3.0 [272] Physics
Yasra 2.32 [273] 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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