Difference between revisions of "Installed Software"
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| [[CNVnator]] || 0.2.5 || [http://sv.gersteinlab.org/] || Biology, NGS || X || | | [[CNVnator]] || 0.2.5 || [http://sv.gersteinlab.org/] || Biology, NGS || X || | ||
--> | --> | ||
+ | |- | ||
+ | | [[Coevol]] || 1.3c, 1.4b || [http://megasun.bch.umontreal.ca/People/lartillot/www/downloadcoevol.html] || Biology, Phylogenetics | ||
|- | |- | ||
| [[CoMap]] || 1.4.1 || [http://home.gna.org/comap] || Biology, Genomics | | [[CoMap]] || 1.4.1 || [http://home.gna.org/comap] || Biology, Genomics |
Revision as of 19:16, 8 August 2014
Installed Software List
Last updated 2014-08-08.
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 | |
BRANCH | 1.8.1 | [39] | Biology, NGS, Mapping | |
Bwa | 0.6.1, 0.7.9a, 0.7.10 | [40] | Biology, NGS | |
Camino | 20140723 | [41] | Biology, Neuroscience, Imaging | |
CAP3 | 20120705 | [42] | Biology, sequence assembly | |
CASAVA | 1.8.2 | [43] | Biology, NGS | |
CD-HIT | 4.6 | [44] | Biology, Genomics | |
CDO | 1.6.1 | [45] | Climate | |
CEAS | 1.0.2 | [46] | Biology, Genomics | |
CellProfiler | 2.0 | [47] | Biology, Image Analysis | |
Charmm | 36a3 | [48] | Simulation, Chemistry | |
Chartdirector | 5.1.0 | [49] | Graphics | |
CIMS | 4.1.2 | [50] | Biology, Genomics | |
Circos | 0.63-pre11 | [51] | Biology, Visualization | |
CisGenome | 2.0 | [52] | Biology, Genomics, Peak Calling | |
CLHEP | 2.2.0.1 | [53] | High Energy Physics | |
ClonalFrame | 1.1, 1.2 | [54] | Biology, Genomics, NGS | |
ClustalW | 2.1 | [55] | Biology, Genomics | |
Clview | 20130402 | [56] | Biology, Genomics | |
CMake | 2.8.8 | [57] | Programming, Build System | |
CNVSeq | 20110715 | [58] | Biology, NGS | |
Coevol | 1.3c, 1.4b | [59] | Biology, Phylogenetics | |
CoMap | 1.4.1 | [60] | Biology, Genomics | |
CONCOCT | 0.3.1 | [61] | Biology, Genomics | |
Consed | 23.0 | [62] | Biology, Genomics | |
covNMR | 2014 | [63] | Biochemistry | |
CUDA | 4.2, 5.5 | [64] | Programming, Graphics | |
Cufflinks | 1.3.0, 2.0.2, 2.2.1 | [65] | Biology, NGS | |
Cutadapt | 1.1 | [66] | Biology, NGS | |
DAKOTA | 5.4.0 | [67] | Computational Science | |
DDSCAT | 7.3.0 | [68] | Astrophysics | |
Delft3D | 3621 | [69] | Hydrodynamics, Physics | |
Desmond | 3.0.3.1 | [70] | Simulation, Biology, Chemistry | |
Dalton | 2011 | [71] | Quantum Chemistry | |
DiffReps | 1.55.4 | [72] | Biology, NGS, ChIP-Seq | |
Dindel | 1.01 | [73] | Biology, NGS | |
DIYABC | many | [74] | Biology, Genomics | |
Dlpoly | 4.03.4 | [75] | Simulation, Biology, Chemistry | |
DNA Clust | 3.0 | [76] | Biology, Genomics | |
Dock | 6.5, 6.6 | [77] | Chemistry, ligand binding prediction | |
DSSP | 2.2.1 | [78] | Biology, Molecular Dynamics | |
DTI-TK | 2.3.1 | [79] | Biology, Neurology, Imaging | |
EA-Utils | 1.1.2.537 | [80] | Biology, NGS | |
EIGENSOFT | 4.2, 5.0.1 | [81] | Biology, Population | |
emboss | 6.5.7 | [82] | Biology, multi-tool suite | |
eQTLA | 1.1 | [83] | Biology, Genomics | |
Espresso | 5.0.1 | [84] | Modeling, Physics | |
ESPRIT | 201211 | [85] | Biology, NGS, Metagenomics | |
ETE2 | 2.1 | [86] | Biology, Phylogenetics | |
Eval | 2.2.8 | [87] | Biology, Genomics, GUI | |
ExaML | 1.0.3, 1.0.5, 1.0.12 | [88] | Biology, Phylogenetics | |
Exonerate | 2.2.0 | [89] | Biology, Genomics | |
FAR | 2.15 | [90] | Biology, Genomics | |
FASTA | 34.26.5, 36.3.6d | [91] | Biology, Genomics | |
FastML | 3.0 | [92] | Biology, Phylogenetics, ML | |
FastQC | 0.9.6, 0.10.1 | [93] | Biology, NGS | |
FastTree | 2.1.7 | [94] | Biology, Phylogenetics | |
Fastx_toolkit | 0.0.13.2 | [95] | Biology, NGS | |
fcGENE | 1.0.7 | [96] | Biology, Genomics, SNP | |
Ferret | 6.82 | [97] | Oceanography, Meteorology | |
FFmpeg | 2.1.3 | [98] | Multimedia, audio, video | |
FFTW | 3.3.2, 3.3.3 | [99] | Math, Library, C++ | |
FLASH | 1.2.10 | [100] | Biology, Genomics, NGS | |
Fluent | 14.5.7, 15.0 | [101] | Simulation, Fluid Dynamics | |
FragGeneScan | 1.16 | [102] | Biology, NGS, Genomics | |
FreeBayes | 0.9.6 | [103] | Biology, NGS, SNP Calling | |
Freesurfer | 5.2.0 | [104] | Biology, Neurology, Imaging | |
FSL | 5.0.2.2 | [105] | Biology, Neurology, Imaging | |
Garli | 2.0, 2.01 | [106] | Biology, Phylogenetics | |
GASVPro | 201310 | [107] | Biology, NGS, Genomics | |
GATE | 7.0 | [108] | Data Analysis | |
GATK | 1.6.9, 2.7.4, 3.1.1 | [109] | Biology, NGS | |
Gaussian | E01, G03, G09-A.02, G09-C.01 | [110] | Modeling, Computational Chemistry | |
Geant4 | 4.10 | [111] | Physics | |
GEM | 20130406 | [112] | Biology, NGS | |
GEMINI | 4.6.6a | [113] | Biology, Genomics, Genetics | |
GenBank Tools | 20140130 | [114] | BIology< Genomics | |
GeneMark | 2012.04 | [115] | Biology, Genomics, Metagenomics | |
Genewise | 2.2.0 | [116] | Biology, Genomics, Annotation | |
GenomicTools | 2.7.0 | [117] | Biology, NGS | |
Git | 1.8.2.1 | [118] | Development, Revision Control | |
Gmap | 20130618, 20130720, 20140530 | [119] | Biology, Genomics | |
GnuPlot | 4.6.0 | [120] | Graphics, Plotting, Programming | |
Grace | 5.1.22 | [121] | Graphics, plotting, 2D | |
GrADS | 2.0.1 | [122] | Earth Science | |
GraphViz | 2.38.0 | [123] | Graphics, plotting, visualization | |
Gromacs | 4.5.5, 4.6.5 | [124] | Chemistry, Modeling, Simulation | |
GSL | 1.15 | [125] | Library, Math, C++, C | |
GULP | 4.0 | [126] | Material Science | |
HaMStR | v8b | [127] | Biology, Genomics | |
Hapsembler | 2.21 | [128] | Biology, Genomics, NGS | |
HDF5 | 1.8.9, 1.8.12 | [129] | Library, Data | |
HMMER3 | 3.0 | [130] | Biology, Genomics | |
HMMSplicer | 0.9.5 | [131] | Biology, Genomics | |
HOMER | 4.2 | [132] | Biology, Genomics | |
HTSeq | 0.5.3p3, 0.6.1p1 | [133] | Biology, NGS | |
HyPhy | 2.1.2.28 | [134] | Biology, Phylogenetics | |
Hypre | 1.10.0b, 2.8.0b | [135] | Library, Math, Physics | |
IDBA-UD | 1.0.9, 1.1.0 | [136] | Biology, NGS | |
IM and IMa | 20091217 | [137] | Biology, Population | |
IMa2 | 20120827 | [138] | Biology, Population | |
ImageMagick | 6.8.8-9 | [139] | Image manipulation | |
Intel Compilers | 11.1, 2012 | [140] | Programming, Compilers | |
IOAPI | 3.1 | [141] | Meteorology | |
Iprscan | 4.8 | [142] | Biology, Genomics | |
ITK | 4.3.1 | [143] | Biology, Genomics | |
ITK-SNAP | 3.0.0 | [144] | Biology, Neuroscience, Imaging | |
JAGS | 3.3.0 | [145] | Statistics | |
Java | 1.6.0_31, 1.7.0_02 | [146] | Java Development Kit | |
Kent | 20120524 | [147] | Biology, NGS | |
Kmer | 1934 | [148] | Biology, NGS | |
LAMMPS | 28Oct12, 30Sep13 | [149] | Molecular Dynamics Simulation | |
Last | 193, 247 | [150] | Biology, Sequence alignment | |
Lastz | 1.03.02, 1.02.00 | [151] | Biology, NGS | |
LIBSVM | 3.12 | [152] | Machine Learning | |
LSC | 0.3, 0.3.1 | [153] | Biology, NGS, Error correction | |
Loci | 3.3 | [154] | Fluid Dynamics | |
LS-DYNA | 700, 711 | [155] | Physics | |
MACH | 1.0.18 | [156] | Biology, Genomics | |
MACS | 1.4.2 | [157] | Biology, ChIP-Seq | |
mafft | 7.037, 6.903 | [158] | Biology, Multiple sequence alignment | |
Maker | 2.10, 2.25b | [159] | Biology, Annotation, Genomics | |
Maq | 0.7.1 | [160] | Biology, NGS | |
Matlab | 2012a, 2013a, 2014a | [161] | Math, Simulation, Programming | |
MATS | 2.1.0, 3.0.6b, 3.0.8 | [162] | BIology, NGS | |
MCarts | 1.0.2 | [163] | Biology, Genomics, Markov models | |
MCNP | 5, 6b2 | [164] | Physics | |
MCNPX | 2.7.0, 2.7.0-i8 | [165] | Physics | |
Meme | 4.8.1 | [166] | Biology, Motifs, Sequence analysis | |
Mercurial | 2.7 | [167] | Development, Revision Control | |
Metabin | 1.0 | [168] | Biology, Metagenomics | |
MetaCluster | 5.0beta | [169] | Biology, Metagenomics | |
MetaVelvet | 1.2.01 | [170] | Biology, NGS | |
MetaGeneMark | 2012.04 | [171] | Biology, Genomics | |
Mfold | 3.6 | [172] | Biology, Genomics | |
Midnight Commander | 4.6.1 | [173] | Tools, Utilities | |
Migrate-n | 3.3.0 | [174] | Biology, Population | |
mira | 3.2.0, 3.4.0.1, 3.9.9, 3.9.18, 4.0.rc1 | [175] | Biology, NGS | |
MISO | 0.4.4, 0.4.9 | [176] | Biology, NGS | |
MSMBuilder | 2.5.1 | [177] | Molecular Dynamics | |
Modeller | 9.11, 9.13, 9.14 | [178] | Biology, Modeling | |
Molden | 5.0 | [179] | Molecular, electronic structure | |
mosaik | 2.1.33 | [180] | Biology,NGS | |
Mothur | 1.31.2 | [181] | Biology, Microbial Ecology | |
MP-EST | 1.4 | [182] | Biology, Phylogenetics | |
mpiP | 3.4.1 | [183] | Parallel Computing | |
MrBayes | 3.2.1 | [184] | Biology, Phylogenetics | |
MRIcron | 201306 | [185] | Biology, MRI, Imaging | |
MUMmer | 3.23 | [186] | Biology, Genomics | |
MUSCLE | 3.8.31 | [187] | Biology, Genomics | |
NAMD | 2.9 | [188] | Simulation, Chemistry, Biology | |
Nbody | 6 | [189] | Astronomy | |
NCBI C++ Toolkit | 12.0.0 | [190] | Biology, C++, Development | |
NCL | 6.1.2 | [191] | Atmosphere Science | |
NCO | 4.2.1, 4.4.3 | [192] | Data exchange tools | |
NetCDF | 4.2 | [193] | Data exchange, Tools | |
Newbler | 2.6, 2.7 | [194] | Biology, NGS | |
Nexus NCL | 2.1.18 | [195] | Biology, Phylogenetics, Library | |
NMRPipe | 7.9 | [196] | Biology, Biochemistry | |
Novoalign | 2.08.02, 3.00.02 | [197] | Biology, NGS | |
Oases | 0.2.08 | [198] | Biology, NGS | |
Olego | 1.1.2, 1.1.5 | [199] | Biology, NGS, RNA-Seq | |
Octave | 3.6.4 | [200] | Numerical Computation | |
OpenBabel | 2.3.2 | [201] | Biology, Chemistry | |
OpenCV | 2.4.8 | [202] | Computervision | |
OpenFOAM | 2.1.1 | [203] | Fluid Dynamics | |
OrthoMCL | 2.0.2, 2.0.3, 2.0.7 | [204] | Biology, Genomics | |
PAML | 4.7 | [205] | Biology, Phylogenetics | |
ParaView | 4.1.0 | [206] | Data Analysis | |
PartitionFinder | 1.0.1, 1.1.1 | [207] | Biology, Phylogenetics, Evolution | |
Parflow | v615 | [208] | Ecology, Modeling | |
PASA | 1.5, 2.0-r20130605p1, 2.0-r20130907 | [209] | Biology, Genomics | |
PeakSplitter | 1.0 | [210] | Biology, Chip-Seq | |
PDT | 3.18 | [211] | Programming, Profiler | |
Perl | 5.16.0 | [212] | Programming, Language | |
PerM | 0.4.0 | [213] | Biology, NGS | |
PETSc | 2.3, 3.3 | [214] | Math, Numerical solvers | |
Phenix | 1.8.1069 | [215] | Crystallography | |
PHITS | 2.52 | [216] | Physics | |
PhyloBayes | 3.3f, 1.4f MPI | [217] | Biology, Phylogenetics | |
PhyML | 3.0, 20121109 | [218] | Biology, Phylogenetics | |
Picard | 1.69, 1.72, 1.80 | [219] | Biology, NGS | |
Preseq | 0.0.4 | [220] | Biology, NGS | |
ProBABEL | 0.4.2 | [221] | Biology, Genomics, GWAS | |
Proovread | 1.03rcl | [222] | Biology, Genomics, NGS | |
Proteinortho | 4.26 | [223] | Biology, Genomics | |
python | 2.6.8, 2.7.3 | [224] | Programming, scripting, language | |
QIIME | 1.5.0 | [225] | Biology, Ecology | |
QT | 4.8.3 | [226] | Computer Science | |
Quickquartet | 1.0.0 | [227] | Biology, Phylogenetics | |
R | 2.15.1, 2.15.0-mpi, Rmpi/2.15.1, 3.0.0 | [228] | Statistics, Programming | |
R8S | 1.71 | [229] | Biology, Evolution | |
RADICAL | 0.2 | [230] | Biology, Phylogenetics, Genomics | |
RAxML | 7.9.1, 8.0.0, 8.0.25 | [231] | Biology, Phylogenetics | |
RepeatMasker | 3.3.0 | [232] | Biology, Genomics | |
Reptile | 1.1 | [233] | Biology, NGS, error correction | |
riboPicker | 0.4.3 | [234] | Biology, Sequence | |
RNAhybrid | 2.1.1 | [235] | Biology, Genomics | |
ROOT | 6.0 | [236] | Data Analysis | |
RSEG | 0.4.8 | [237] | Biology, NGS | |
Sailfish | 0.6.3 | [238] | Biology, NGS, RNA-Seq | |
samtools | 0.1.16, 0.1.18, 0.1.19 | [239] | Biology, NGS | |
SAS | 9.3 | [240] | Statistics, Graphing | |
SATe | 2.2.7 | [241] | Biology, Phylogenetics | |
Sharcgs | 1.2.11 | [242] | Biology, NGS, de novo assembly | |
Schrodinger | 2012, 2013 | [243] | Simulation, chemistry | |
SCons | 2.3.0 | [244] | Programming, Build System | |
SeqPrep | 0.5 | [245] | Biology, NGS | |
SEQuel | 1.0.1 | [246] | Biology, NGS | |
Seqtk | 20140729 | [247] | Biology, NGS | |
SeqyClean | 1.8.10 | [248] | Biology, NGS, quality filter | |
Sickle | 1.200 | [249] | Biology, NGS, quality filter | |
Siesta | 2.0.2,3.1 | [250] | Simulation, Physics, Ab Initio | |
SIFT | 4.0.3b | [251] | Biology, Genomics | |
Silo | 4.7 | [252] | Library, Data | |
Slicer | 4.3.1 | [253] | Biology, Imaging | |
SMALT | 0.7.6 | [254] | Biology, NGS | |
Snap | 20100728 | [255] | Biology, Genomics | |
SOAPdenovo | 1.05 | [256] | Biology, NGS | |
SOAPdenovo-Trans | 1.01, 1.03 | [257] | Biology, NGS | |
SparCC | 201402 | [258] | Microbial Ecology | |
Spades | 2.5.0, 2.5.1, 3.0.0 | [259] | Biology, NGS | |
Spanki | 0.4.1, 0.4.3 | [260] | Biology, NGS, RNA-Seq | |
SPARTA+ | 2.60 | [261] | Chemistry | |
SPIMAP | 1.1 | [262] | Biology, Phylogenetics | |
SpliceTrap | 0.90.5 | [263] | Biology, NGS, RNA-Seq | |
SPM | 8 | [264] | Biology, Statistics, Neurology, Imaging | |
Sputnik | 1.0 | [265] | Biology, Genomics | |
SRA | 2.1.10 | [266]] | biology, NGS | |
SSPACE | 2.0 | [267] | Biology, NGS | |
Stacks | 0.9995 | [268] | Biology, Genomics, NGS | |
STAR | 2.3.0e | [269] | Biology, NGS, Alignment | |
STAR-CCM+ | 8.06 | [270] | Mechanical Engineering | |
Stata | 10.1, 13 | [271] | Statistics, Data analysis | |
Stringtie | 0.97 | [272] | Biology, NGS, Alignment | |
Structure | 2.3.3, 2.3.4 | [273] | Biology, Population | |
SUNDIALS | 2.3.0, 2.5.0 | [274] | Numerical Solver | |
swak4Foam | 2.x | [275] | Fluid Dynamics | |
Swig | 2.0.9 | [276] | Programming, C, C++, Python | |
Syzygy | 1.2.7 | [277] | Biology, Genomics | |
TAU | 2.21.4, 2.23 | [278] | Profiling, Tracing, Programming | |
T-Coffee | 9.03.r1318 | [279] | Biology, Genomics, Multiple Alignment | |
TESS | 2.3.1 | [280] | Biology, Genomics, Markov | |
tgicl | 2.1 | [281] | Biology, sequencing, clustering | |
Tophat | 1.4.1, 2.0.1, 2.0.8b | [282] | Biology, NGS | |
Totalview | 8.12.0 | [283] | Computer Science | |
TPP | 4.7.0 | [284] | Bioinformatics, MassSpec | |
TreeFix | 1.1.7 | [285] | Biology, Phylogenetics | |
TRF | 4.04 | [286] | Biology, Genomics | |
Trilinos | 11.4.1, 11.8.1 | [287] | Math Algorithm | |
Trimmomatic | 0.22, 0.32 | [288] | Biology, NGS | |
Trinity | r20131110, r20140413 | [289] | Biology, NGS, RNA-Seq | |
Twinscan | 4.1.2 | [290] | Biology, Genomics | |
usearch | 5.2.32, 7.0.959, 7.0.1001-64 (licensed 64-bit) | [291] | Biology, Sequence analysis | |
Valgrind | 3.9.0 | [292] | Computer Science | |
VASP | 4.6.34, 5.2.12, 5.3.2, 5.3.3 | [293] | Quantum Chemistry, Ab Initio | |
VCFtools | 0.1.9, 0.1.10 | [294] | Biology, SNPs | |
velvet | 1.2.06, 1.2.07, 1.2.10 | [295] | Biology, NGS | |
vmd | 1.9.1 | [296] | Biology, Visualization | |
Wannier90 | 1.2, 2.0.0 | [297] | Computational Physics | |
WebLogo | 3.3 | [298] | Biology, Genomics | |
WDSSII | 1 | [299] | Meteorology | |
WIEN2k | 12.1 | [300] | Material Science, Chemistry | |
wgs | 7.0.1.22 | [301] | Biology, NGS | |
wublast | 2.0 | [302] | Biology, Sequence Alignment | |
Yambo | 3.3.0 | [303] | Physics | |
Yasra | 2.32 | [304] | Biology, NGS |
- ↑ 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.