Difference between revisions of "Installed Software"

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| [[Ima2|IMa2]] || 20120827 || [http://genfaculty.rutgers.edu/hey/software#IMa2]||Biology, Population
 
| [[Ima2|IMa2]] || 20120827 || [http://genfaculty.rutgers.edu/hey/software#IMa2]||Biology, Population
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| [[ImageJ]] || 1.48 || [http://rsbweb.nih.gov/ij] || Image manipulation
 
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| [[ImageMagick]] || 6.8.8-9 || [http://imagemagick.org/] || Image manipulation
 
| [[ImageMagick]] || 6.8.8-9 || [http://imagemagick.org/] || Image manipulation

Revision as of 15:46, 19 September 2014

Installed Software List

Last updated 2014-09-19.

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
ARC 20140312 [11] Biology, NGS
AtomEye 3 [12] Material Science
ATRAM 20140624 [13] Biology, NGS
Augustus 2.6 [14] Biology, NGS
BamBam 1.0 [15] Biology, NGS
Bamstats 20140602 [16] Biology, NGS
Bamtools 2.1.1 [17] Biology, NGS
BamUtil 1.0.2 [18] Biology, NGS
BayesRate 1.3.43 [19] Biology, Phylogenetics
Bbcp 12.08.17.00.0 [20] Network file transfer
Bcftools 20140618 [21] Biology, Genomics, NGS
BEAGLE 3.2.2 [22] Biology, Genetics, Genotyping
BEAST 1.7.5, 2.0.1, 2.0.2.pre [23] Biology, Phylogenetics
BEDTools 2.16.2, 2.17.0 [24] Biology, NGS
BEST 2.3 [25] Biology, Phylogenetics
BETA 1.0.5 [26] Biology, NGS
BFAST 0.7.0 [27] Biology, NGS
Bismark 0.7.4, 0.7.7 [28] Biology, Methylation, NGS
Bioconductor Latest [29] Biology, R, Statistics
BioPerl 1.006901 [30] Biology, Perl
BioPython 1.59 [31] Biology, Python
BLASR 20130815 [32] Biology, NGS
NCBI BLAST 2.2.27, 2.2.28, 2.2.29 [33] Biology, Sequence alignment
Blast2go 2.5.0-20120705 [34] Biology, Annotation
BLAT 20120524 [35] Biology, Sequence alignment
Blender 2.63 [36] Graphics
Boost 1.49.0, 1.53.0, 1.54.0 [37] C++, Library
Bowtie 0.12.8, 0.12.9, 1.0.0 [38] Biology, NGS
Bowtie2 2.1.0, 2.2.2, 2.2.3 [39] Biology, NGS
BPP 2.2, 1.9.0 [40] Biology, Phylogenetics
BRANCH 1.8.1 [41] Biology, NGS, Mapping
Bwa 0.6.1, 0.7.9a, 0.7.10 [42] Biology, NGS
Camino 20140723 [43] Biology, Neuroscience, Imaging
CAP3 20120705 [44] Biology, sequence assembly
CASAVA 1.8.2 [45] Biology, NGS
CD-HIT 4.6 [46] Biology, Genomics
CDO 1.6.1 [47] Climate
CEAS 1.0.2 [48] Biology, Genomics
CellProfiler 2.0 [49] Biology, Image Analysis
CGATools 1.6.0.42 [50] Biology, NGS
Charmm 36a3 [51] Simulation, Chemistry
Chartdirector 5.1.0 [52] Graphics
Chimera 1.7 [53] Biology, Modeling
CIMS 4.1.2 [54] Biology, Genomics
Circos 0.63-pre11 [55] Biology, Visualization
CisGenome 2.0 [56] Biology, Genomics, Peak Calling
CLHEP 2.2.0.1 [57] High Energy Physics
ClonalFrame 1.1, 1.2 [58] Biology, Genomics, NGS
ClustalW 2.1 [59] Biology, Genomics
Cluster3 1.52 [60]] Biology, Genomics
Clview 20130402 [61] Biology, Genomics
CMake 2.8.8 [62] Programming, Build System
CNVSeq 20110715 [63] Biology, NGS
Coevol 1.3c, 1.4b [64] Biology, Phylogenetics
CoMap 1.4.1 [65] Biology, Genomics
CONCOCT 0.3.1 [66] Biology, Genomics
Consed 23.0 [67] Biology, Genomics
covNMR 2014 [68] Biochemistry
CUDA 4.2, 5.5 [69] Programming, Graphics
Cufflinks 1.3.0, 2.0.2, 2.2.1 [70] Biology, NGS
Cutadapt 1.1 [71] Biology, NGS
DAKOTA 5.4.0 [72] Computational Science
DCMTK 3.6.0 [73] Biology, Neuroscience, Imaging
DDSCAT 7.3.0 [74] Astrophysics
DDT 4.1.0, 4.2.1 [75] Software
Delft3D 3621 [76] Hydrodynamics, Physics
Desmond 3.0.3.1 [77] Simulation, Biology, Chemistry
Dalton 2011 [78] Quantum Chemistry
DiffReps 1.55.4 [79] Biology, NGS, ChIP-Seq
Dindel 1.01 [80] Biology, NGS
DIYABC 1.0.4.43b, 2.0.3 [81] Biology, Genomics
Dlpoly 4.03.4 [82] Simulation, Biology, Chemistry
DNA Clust 3.0 [83] Biology, Genomics
Dock 6.5, 6.6 [84] Chemistry, ligand binding prediction
DOT 2.0 [85] Biology, Bioinformatics, Docking
Doxygen 1.8.3.1 [86] Programming, Documentation
DSSP 2.2.1 [87] Biology, Molecular Dynamics
DTI-TK 2.3.1 [88] Biology, Neurology, Imaging
EA-Utils 1.1.2.537 [89] Biology, NGS
ECTools 20140311 [90] Biology, Sequencing, Bioinformatics
EEGLAB 12.0.2.1b [91] Biology, Matlab
EIGENSOFT 4.2, 5.0.1 [92] Biology, Population
emboss 6.5.7 [93] Biology, multi-tool suite
EMIRGE 20130727 [94] Biology, NGS
eQTLA 1.1 [95] Biology, Genomics
Eqtlbma 1.2.2 [96] Biology, Genotyping
Espresso 5.0.1 [97] Modeling, Physics
ESPRIT 201211 [98] Biology, NGS, Metagenomics
ETE2 2.1 [99] Biology, Phylogenetics
Eval 2.2.8 [100] Biology, Genomics, GUI
ExaBayes 1.2.1 [101] Biology, Phylogenetics
ExaML 1.0.3, 1.0.5, 1.0.12 [102] Biology, Phylogenetics
Exonerate 2.2.0 [103] Biology, Genomics
eXpress 1.3.1 [104] Biology, NGS
FAR 2.15 [105] Biology, Genomics
FASTA 34.26.5, 36.3.6d [106] Biology, Genomics
FastML 3.0 [107] Biology, Phylogenetics, ML
FastQC 0.9.6, 0.10.1 [108] Biology, NGS
FastTree 2.1.7 [109] Biology, Phylogenetics
Fastx_toolkit 0.0.13.2 [110] Biology, NGS
fcGENE 1.0.7 [111] Biology, Genomics, SNP
Ferret 6.82 [112] Oceanography, Meteorology
FFmpeg 2.1.3 [113] Multimedia, audio, video
FFTW 3.3.2, 3.3.3 [114] Math, Library, C++
FLASH 1.2.10 [115] Biology, Genomics, NGS
Flexbar 2.3 [116] Biology, Genomics, NGS
Fluent 14.5.7, 15.0 [117] Simulation, Fluid Dynamics
FragGeneScan 1.16 [118] Biology, NGS, Genomics
FreeBayes 0.9.6, 0.9.15 [119] Biology, NGS, SNP Calling
Freesurfer 5.2.0 [120] Biology, Neurology, Imaging
FSL 5.0.2.2 [121] Biology, Neurology, Imaging
GapFiller 1.11 [122] Biology, NGS
Garli 2.0, 2.01 [123] Biology, Phylogenetics
GASVPro 201310 [124] Biology, NGS, Genomics
GATE 7.0 [125] Data Analysis
GATK 1.6.9, 2.7.4, 3.1.1 [126] Biology, NGS
Gaussian E01, G03, G09-A.02, G09-C.01 [127] Modeling, Computational Chemistry
Geant4 4.10 [128] Physics
GEM 20130406 [129] Biology, NGS
GEMINI 4.6.6a [130] Biology, Genomics, Genetics
GenBank Tools 20140130 [131] BIology< Genomics
GeneMark 2012.04 [132] Biology, Genomics, Metagenomics
Genewise 2.2.0 [133] Biology, Genomics, Annotation
GenomicTools 2.7.0 [134] Biology, NGS
Git 1.8.2.1 [135] Development, Revision Control
Gmap 20130618, 20130720, 20140530 [136] Biology, Genomics
GNU 4.4.6, 4.7.2 [137] Compilers, Programming
GnuPlot 4.6.0 [138] Graphics, Plotting, Programming
Grace 5.1.22 [139] Graphics, plotting, 2D
GrADS 2.0.1 [140] Earth Science
GraphViz 2.38.0 [141] Graphics, plotting, visualization
Gromacs 4.5.5, 4.6.5 [142] Chemistry, Modeling, Simulation
GSNP 1.0 [143] Biology, Bioinformatics, NGS
GSL 1.15 [144] Library, Math, C++, C
GULP 4.0 [145] Material Science
HaMStR v8b [146] Biology, Genomics
Hapsembler 2.21 [147] Biology, Genomics, NGS
HDF5 1.8.9, 1.8.12 [148] Library, Data
HMMER3 3.0 [149] Biology, Genomics
HMMSplicer 0.9.5 [150] Biology, Genomics
HOMER 4.2 [151] Biology, Genomics
HTMLDoc 1.2.82 [152] Documentation, PDF, HTML
HTSeq 0.5.3p3, 0.6.1p1 [153] Biology, NGS
HyPhy 2.1.2.28 [154] Biology, Phylogenetics
Hypre 1.10.0b, 2.8.0b [155] Library, Math, Physics
IDBA-UD 1.0.9, 1.1.0 [156] Biology, NGS
iGTP 1.1 [157] Biology, Bioinformatics, Phylogenetics
IM and IMa 20091217 [158] Biology, Population
IMa2 20120827 [159] Biology, Population
ImageJ 1.48 [160] Image manipulation
ImageMagick 6.8.8-9 [161] Image manipulation
Intel Compilers 11.1, 2012 [162] Programming, Compilers
IOAPI 3.1 [163] Meteorology
Iprscan 4.8 [164] Biology, Genomics
ITK 4.3.1 [165] Biology, Genomics
ITK-SNAP 3.0.0 [166] Biology, Neuroscience, Imaging
JAGS 3.3.0 [167] Statistics
Java 1.6.0_31, 1.7.0_02 [168] Java Development Kit
Kent 20120524 [169] Biology, NGS
Khmer 1.1 [170] Biology, NGS
Kmer 1934 [171] Biology, NGS
KmerGenie 1.6741 [172] Biology, NGS, Utilities
LAMMPS 28Oct12, 30Sep13 [173] Molecular Dynamics Simulation
Last 193, 247 [174] Biology, Sequence alignment
Lastz 1.03.02, 1.02.00 [175] Biology, NGS
LIBSVM 3.12 [176] Machine Learning
LSC 0.3, 0.3.1 [177] Biology, NGS, Error correction
Loci 3.3 [178] Fluid Dynamics
LS-DYNA 700, 711 [179] Physics
MACH 1.0.18 [180] Biology, Genomics
MACS 1.4.2 [181] Biology, ChIP-Seq
mafft 7.037, 6.903 [182] Biology, Multiple sequence alignment
Maker 2.10, 2.25b [183] Biology, Annotation, Genomics
Maq 0.7.1 [184] Biology, NGS
Matlab 2012a, 2013a, 2014a [185] Math, Simulation, Programming
MATS 2.1.0, 3.0.6b, 3.0.8 [186] BIology, NGS
MCarts 1.0.2 [187] Biology, Genomics, Markov models
MCNP 5, 6b2 [188] Physics
MCNPX 2.7.0, 2.7.0-i8 [189] Physics
Meme 4.8.1 [190] Biology, Motifs, Sequence analysis
Mercurial 2.7 [191] Development, Revision Control
Metabin 1.0 [192] Biology, Metagenomics
MetaCluster 5.0beta [193] Biology, Metagenomics
MetaCV 2.3.0 [194] Biology, NGS
MetaVelvet 1.2.01 [195] Biology, NGS
MetaGeneMark 2012.04 [196] Biology, Genomics
Mfold 3.6 [197] Biology, Genomics
Midnight Commander 4.6.1 [198] Tools, Utilities
Migrate-n 3.3.0 [199] Biology, Population
mira 3.2.0, 3.4.0.1, 3.9.9, 3.9.18, 4.0.rc1 [200] Biology, NGS
MISO 0.4.4, 0.4.9 [201] Biology, NGS
MSMBuilder 2.5.1 [202] Molecular Dynamics
Modeller 9.11, 9.13, 9.14 [203] Biology, Modeling
Molden 5.0 [204] Molecular, electronic structure
mosaik 2.1.33 [205] Biology,NGS
Mothur 1.31.2 [206] Biology, Microbial Ecology
MP-EST 1.4 [207] Biology, Phylogenetics
mpiP 3.4.1 [208] Parallel Computing
MrBayes 3.2.1 [209] Biology, Phylogenetics
MRIcron 201306 [210] Biology, MRI, Imaging
MUMmer 3.23 [211] Biology, Genomics
MUSCLE 3.8.31 [212] Biology, Genomics
NAMD 2.9 [213] Simulation, Chemistry, Biology
Nbody 6 [214] Astronomy
NCBI C++ Toolkit 12.0.0 [215] Biology, C++, Development
NCL 6.1.2 [216] Atmosphere Science
NCO 4.2.1, 4.4.3 [217] Data exchange tools
Ncview 2.1.2 [218] Data visualization
NetCDF 3.4.2, 4.2, 4.3 [219] Data exchange, Tools
Newbler 2.6, 2.7 [220] Biology, NGS
Nexus NCL 2.1.18 [221] Biology, Phylogenetics, Library
NMRPipe 7.9 [222] Biology, Biochemistry
Novoalign 2.08.02, 3.00.02 [223] Biology, NGS
Oases 0.2.08 [224] Biology, NGS
Olego 1.1.2, 1.1.5 [225] Biology, NGS, RNA-Seq
Octave 3.6.4 [226] Numerical Computation
OpenBabel 2.3.2 [227] Biology, Chemistry
OpenCV 2.4.8 [228] Computervision
OpenFOAM 2.1.1 [229] Fluid Dynamics
OrthoMCL 2.0.2, 2.0.3, 2.0.7 [230] Biology, Genomics
PAML 4.7 [231] Biology, Phylogenetics
ParaView 4.1.0 [232] Data Analysis
PartitionFinder 1.0.1, 1.1.1 [233] Biology, Phylogenetics, Evolution
Parflow v615 [234] Ecology, Modeling
PASA 1.5, 2.0-r20130605p1, 2.0-r20130907 [235] Biology, Genomics
PBJelly 14.7.14 [236] Biology, Bioinformatics
PeakSplitter 1.0 [237] Biology, Chip-Seq
PDT 3.18 [238] Programming, Profiler
Perl 5.16.0 [239] Programming, Language
PerM 0.4.0 [240] Biology, NGS
PETSc 2.3, 3.3 [241] Math, Numerical solvers
Phenix 1.8.1069 [242] Crystallography
PHITS 2.52 [243] Physics
PhyloBayes 3.3f, 1.4f MPI [244] Biology, Phylogenetics
PhyML 3.0, 20121109 [245] Biology, Phylogenetics
Picard 1.69, 1.72, 1.80 [246] Biology, NGS
Preseq 0.0.4 [247] Biology, NGS
ProBABEL 0.4.2 [248] Biology, Genomics, GWAS
Proovread 1.03rcl [249] Biology, Genomics, NGS
Proteinortho 4.26 [250] Biology, Genomics
python 2.6.8, 2.7.3 [251] Programming, scripting, language
QIIME 1.5.0 [252] Biology, Ecology
QT 4.8.3 [253] Computer Science
Quickquartet 1.0.0 [254] Biology, Phylogenetics
R 2.15.1, 2.15.0-mpi, Rmpi/2.15.1, 3.0.0 [255] Statistics, Programming
R8S 1.71 [256] Biology, Evolution
RADICAL 0.2 [257] Biology, Phylogenetics, Genomics
RAxML 7.9.1, 8.0.0, 8.0.25 [258] Biology, Phylogenetics
RepeatMasker 3.3.0 [259] Biology, Genomics
Reptile 1.1 [260] Biology, NGS, error correction
riboPicker 0.4.3 [261] Biology, Sequence
RNAhybrid 2.1.1 [262] Biology, Genomics
ROOT 6.0 [263] Data Analysis
RSEG 0.4.8 [264] Biology, NGS
Sailfish 0.6.3 [265] Biology, NGS, RNA-Seq
samtools 0.1.16, 0.1.18, 0.1.19 [266] Biology, NGS
SAS 9.3 [267] Statistics, Graphing
SATe 2.2.7 [268] Biology, Phylogenetics
Sharcgs 1.2.11 [269] Biology, NGS, de novo assembly
Schrodinger 2012, 2013 [270] Simulation, chemistry
SeqPrep 0.5 [271] Biology, NGS
SEQuel 1.0.1 [272] Biology, NGS
Seqtk 20140729 [273] Biology, NGS
SeqyClean 1.8.10 [274] Biology, NGS, quality filter
Sickle 1.200 [275] Biology, NGS, quality filter
Siesta 2.0.2,3.1 [276] Simulation, Physics, Ab Initio
SIFT 4.0.3b [277] Biology, Genomics
Silo 4.7 [278] Library, Data
Slicer 4.3.1 [279] Biology, Imaging
SMALT 0.7.6 [280] Biology, NGS
Snap 20100728 [281] Biology, Genomics
SOAPdenovo 1.05 [282] Biology, NGS
SOAPdenovo-Trans 1.01, 1.03 [283] Biology, NGS
SparCC 201402 [284] Microbial Ecology
Spades 2.5.0, 2.5.1, 3.0.0 [285] Biology, NGS
Spanki 0.4.1, 0.4.3 [286] Biology, NGS, RNA-Seq
SPARTA+ 2.60 [287] Chemistry
SPIMAP 1.1 [288] Biology, Phylogenetics
SpliceTrap 0.90.5 [289] Biology, NGS, RNA-Seq
SPM 8 [290] Biology, Statistics, Neurology, Imaging
Sputnik 1.0 [291] Biology, Genomics
SRA 2.1.10 [292]] biology, NGS
SSPACE 2.0 [293] Biology, NGS
Stacks 0.9995 [294] Biology, Genomics, NGS
STAR 2.3.0e [295] Biology, NGS, Alignment
STAR-CCM+ 8.06 [296] Mechanical Engineering
Stata 10.1, 13 [297] Statistics, Data analysis
Stringtie 0.97 [298] Biology, NGS, Alignment
Structure 2.3.3, 2.3.4 [299] Biology, Population
SUNDIALS 2.3.0, 2.5.0 [300] Numerical Solver
swak4Foam 2.x [301] Fluid Dynamics
swarm 1.2.11 [302] Data Analysis
Swig 2.0.9 [303] Programming, C, C++, Python
Syzygy 1.2.7 [304] Biology, Genomics
TASSEL 5.0 [305] Biology, Genomics
TAU 2.21.4, 2.23 [306] Profiling, Tracing, Programming
T-Coffee 9.03.r1318 [307] Biology, Genomics, Multiple Alignment
TESS 2.3.1 [308] Biology, Genomics, Markov
tgicl 2.1 [309] Biology, sequencing, clustering
Tophat 1.4.1, 2.0.1, 2.0.8b [310] Biology, NGS
Totalview 8.12.0 [311] Computer Science
TPP 4.7.0 [312] Bioinformatics, MassSpec
TrackTools 2011 [313] Bioinformatics
TreeFix 1.1.7 [314] Biology, Phylogenetics
TRF 4.04 [315] Biology, Genomics
Trilinos 11.4.1, 11.8.1 [316] Math Algorithm
Trimmomatic 0.22, 0.32 [317] Biology, NGS
Trinity r20131110, r20140413 [318] Biology, NGS, RNA-Seq
Twinscan 4.1.2 [319] Biology, Genomics
usearch 5.2.32, 7.0.959, 7.0.1001-64 (licensed 64-bit) [320] Biology, Sequence analysis
Valgrind 3.9.0 [321] Computer Science
VASP 4.6.34, 5.2.12, 5.3.2, 5.3.3, 5.3.5 [322] Quantum Chemistry, Ab Initio
VCFtools 0.1.9, 0.1.10 [323] Biology, SNPs
velvet 1.2.06, 1.2.07, 1.2.10 [324] Biology, NGS
vmd 1.9.1 [325] Biology, Visualization
Wannier90 1.2, 2.0.0 [326] Computational Physics
WebLogo 3.3 [327] Biology, Genomics
WDSSII 1 [328] Meteorology
WIEN2k 12.1 [329] Material Science, Chemistry
Wgs or Celera 7.0.1.22 [330] Biology, NGS
wublast 2.0 [331] Biology, Sequence Alignment
Yambo 3.3.0 [332] Physics
Yasra 2.32 [333] 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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