Difference between revisions of "Installed Software"
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| [[MATS]] || 2.1.0, 3.0.6b, '''3.0.8''' || [http://rnaseq-mats.sourceforge.net/index.html]||BIology, NGS | | [[MATS]] || 2.1.0, 3.0.6b, '''3.0.8''' || [http://rnaseq-mats.sourceforge.net/index.html]||BIology, NGS | ||
|- | |- | ||
| − | | [[ | + | | [[MCarts]] || 1.0 || [http://sourceforge.net/projects/mcarts/]||Biology, Genomics, Markov models |
|- | |- | ||
| − | |||
| [[MCL]] || 11-335 || [http://www.micans.org/mcl/] || Biology, Genomics, Clustering|| X || | | [[MCL]] || 11-335 || [http://www.micans.org/mcl/] || Biology, Genomics, Clustering|| X || | ||
| − | |- | + | |- |
| [[MCNP]] || 5, 6b2 || [http://mcnp-green.lanl.gov/about_mcnp5.html/] || Physics | | [[MCNP]] || 5, 6b2 || [http://mcnp-green.lanl.gov/about_mcnp5.html/] || Physics | ||
|- | |- | ||
Revision as of 04:43, 24 July 2014
Installed Software List
Last updated 2014-07-24.
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 | ||
| Bcftools | 20140618 | [18]] | Biology, Genomics, NGS | ||
| BEAGLE | 3.2.2 | [19] | Biology, Genetics, Genotyping | ||
| BEAST | 1.7.5, 2.0.1, 2.0.2.pre | [20] | Biology, Phylogenetics | ||
| BEDTools | 2.16.2, 2.17.0 | [21] | Biology, NGS | ||
| BEST | 2.3 | [22] | Biology, Phylogenetics | ||
| BETA | 1.0.5 | [23] | Biology, NGS | ||
| BFAST | 0.7.0 | [24] | Biology, NGS | ||
| Bismark | 0.7.4, 0.7.7 | [25] | Biology, Methylation, NGS | ||
| Bioconductor | Latest | [26] | Biology, R, Statistics | ||
| BioPerl | 1.006901 | [27] | Biology, Perl | ||
| BioPython | 1.59 | [28] | Biology, Python | ||
| BLASR | 20130815 | [29] | Biology, NGS | ||
| NCBI BLAST | 2.2.27, 2.2.28, 2.2.29 | [30] | Biology, Sequence alignment | ||
| Blast2go | 2.5.0-20120705 | [31] | Biology, Annotation | ||
| BLAT | 20120524 | [32] | Biology, Sequence alignment | ||
| Boost | 1.49.0, 1.53.0, 1.54.0 | [33] | C++, Library | ||
| Bwa | 0.6.1, 0.7.9a, 0.7.10 | [34] | Biology, NGS | ||
| Bowtie | 0.12.8, 0.12.9, 1.0.0 | [35] | Biology, NGS | ||
| Bowtie2 | 2.1.0, 2.2.2, 2.2.3 | [36] | Biology, NGS | ||
| CAP3 | 20120705 | [37] | Biology, sequence assembly | ||
| CASAVA | 1.8.2 | [38] | Biology, NGS | ||
| CD-HIT | 4.6 | [39] | Biology, Genomics | ||
| CDO | 1.6.1 | [40] | Climate | ||
| CEAS | 1.0.2 | [41] | Biology, Genomics | ||
| CellProfiler | 2.0 | [42] | Biology, Image Analysis | ||
| Charmm | 36a3 | [43] | Simulation, Chemistry | ||
| Circos | 0.63-pre11 | [44] | Biology, Visualization | ||
| CisGenome | 2.0 | [45] | Biology, Genomics, Peak Calling | ||
| CLHEP | 2.2.0.1 | [46] | High Energy Physics | ||
| ClustalW | 2.1 | [47] | Biology, Genomics | ||
| Clview | 20130402 | [48] | Biology, Genomics | ||
| CMake | 2.8.8 | [49] | Programming, Build System | ||
| CoMap | 1.4.1 | [50] | Biology, Genomics | ||
| CONCOCT | 0.3.1 | [51] | Biology, Genomics | ||
| Consed | 23.0 | [52] | Biology, Genomics | ||
| covNMR | 2014 | [53] | Biochemistry | ||
| CUDA | 4.2, 5.5 | [54] | Programming, Graphics | ||
| Cufflinks | 1.3.0, 2.0.2, 2.2.1 | [55] | Biology, NGS | ||
| Cutadapt | 1.1 | [56] | Biology, NGS | ||
| DAKOTA | 5.4.0 | [57] | Computational Science | ||
| DDSCAT | 7.3.0 | [58] | Astrophysics | ||
| Delft3D | 3621 | [59] | Hydrodynamics, Physics | ||
| Desmond | 3.0.3.1 | [60] | Simulation, Biology, Chemistry | ||
| Dalton | 2011 | [61] | Quantum Chemistry | ||
| DiffReps | 1.55.4 | [62] | Biology, NGS, ChIP-Seq | ||
| Dindel | 1.01 | [63] | Biology, NGS | ||
| DIYABC | many | [64] | Biology, Genomics | ||
| Dlpoly | 4.03.4 | [65] | Simulation, Biology, Chemistry | ||
| DNA Clust | 3.0 | [66] | Biology, Genomics | ||
| Dock | 6.5, 6.6 | [67] | Chemistry, ligand binding prediction | ||
| DSSP | 2.2.1 | [68] | Biology, Molecular Dynamics | ||
| DTI-TK | 2.3.1 | [69] | Biology, Neurology, Imaging | ||
| EA-Utils | 1.1.2.537 | [70] | Biology, NGS | ||
| EIGENSOFT | 4.2, 5.0.1 | [71] | Biology, Population | ||
| emboss | 6.5.7 | [72] | Biology, multi-tool suite | ||
| eQTLA | 1.1 | [73] | Biology, Genomics | ||
| Espresso | 5.0.1 | [74] | Modeling, Physics | ||
| ESPRIT | 201211 | [75] | Biology, NGS, Metagenomics | ||
| ETE2 | 2.1 | [76] | Biology, Phylogenetics | ||
| Eval | 2.2.8 | [77] | Biology, Genomics, GUI | ||
| ExaML | 1.0.3, 1.0.5, 1.0.12 | [78] | Biology, Phylogenetics | ||
| Exonerate | 2.2.0 | [79] | Biology, Genomics | ||
| FAR | 2.15 | [80] | Biology, Genomics | ||
| FASTA | 34.26.5, 36.3.6d | [81] | Biology, Genomics | ||
| FastML | 3.0 | [82] | Biology, Phylogenetics, ML | ||
| FastQC | 0.9.6, 0.10.1 | [83] | Biology, NGS | ||
| FastTree | 2.1.7 | [84] | Biology, Phylogenetics | ||
| Fastx_toolkit | 0.0.13.2 | [85] | Biology, NGS | ||
| fcGENE | 1.0.7 | [86] | Biology, Genomics, SNP | ||
| Ferret | 6.82 | [87] | Oceanography, Meteorology | ||
| FFmpeg | 2.1.3 | [88] | Multimedia, audio, video | ||
| FFTW | 3.3.2, 3.3.3 | [89] | Math, Library, C++ | ||
| FLASH | 1.2.10 | [90] | Biology, Genomics, NGS | ||
| Fluent | 14.5.7, 15.0 | [91] | Simulation, Fluid Dynamics | ||
| FragGeneScan | 1.16 | [92] | Biology, NGS, Genomics | ||
| FreeBayes | 0.9.6 | [93] | Biology, NGS, SNP Calling | ||
| Freesurfer | 5.2.0 | [94] | Biology, Neurology, Imaging | ||
| FSL | 5.0.2.2 | [95] | Biology, Neurology, Imaging | ||
| Garli | 2.0, 2.01 | [96] | Biology, Phylogenetics | ||
| GASVPro | 201310 | [97] | Biology, NGS, Genomics | ||
| GATE | 7.0 | [98] | Data Analysis | ||
| GATK | 1.6.9, 2.7.4, 3.1.1 | [99] | Biology, NGS | ||
| Gaussian | E01, G03, G09-A.02, G09-C.01 | [100] | Modeling, Computational Chemistry | ||
| Geant4 | 4.10 | [101] | Physics | ||
| GEMINI | 4.6.6a | [102] | Biology, Genomics, Genetics | ||
| GenBank Tools | 20140130 | [103] | BIology< Genomics | ||
| GeneMark | 2012.04 | [104] | Biology, Genomics, Metagenomics | ||
| Genewise | 2.2.0 | [105] | Biology, Genomics, Annotation | ||
| GenomicTools | 2.7.0 | [106] | Biology, NGS | ||
| Git | 1.8.2.1 | [107] | Development, Revision Control | ||
| Gmap | 20130618, 20130720, 20140530 | [108] | Biology, Genomics | ||
| GnuPlot | 4.6.0 | [109] | Graphics, Plotting, Programming | ||
| Grace | 5.1.22 | [110] | Graphics, plotting, 2D | ||
| GrADS | 2.0.1 | [111] | Earth Science | ||
| Gromacs | 4.5.5, 4.6.5 | [112] | Chemistry, Modeling, Simulation | ||
| GSL | 1.15 | [113] | Library, Math, C++, C | ||
| GULP | 4.0 | [114] | Material Science | ||
| HaMStR | v8b | [115] | Biology, Genomics | ||
| HDF5 | 1.8.9, 1.8.12 | [116] | Library, Data | ||
| HMMER3 | 3.0 | [117] | Biology, Genomics | ||
| HMMSplicer | 0.9.5 | [118] | Biology, Genomics | ||
| HOMER | 4.2 | [119] | Biology, Genomics | ||
| HTSeq | 0.5.3p3, 0.6.1p1 | [120] | Biology, NGS | ||
| HyPhy | 2.1.2.28 | [121] | Biology, Phylogenetics | ||
| Hypre | 1.10.0b, 2.8.0b | [122] | Library, Math, Physics | ||
| IDBA-UD | 1.0.9, 1.1.0 | [123] | Biology, NGS | ||
| IM and IMa | 20091217 | [124] | Biology, Population | ||
| IMa2 | 20120827 | [125] | Biology, Population | ||
| ImageMagick | 6.8.8-9 | [126] | Image manipulation | ||
| Intel Compilers | 11.1, 2012 | [127] | Programming, Compilers | ||
| IOAPI | 3.1 | [128] | Meteorology | ||
| Iprscan | 4.8 | [129] | Biology, Genomics | ||
| ITK | 4.3.1 | [130] | Biology, Genomics | ||
| JAGS | 3.3.0 | [131] | Statistics | ||
| Java | 1.6.0_31, 1.7.0_02 | [132] | Java Development Kit | ||
| Kent | 20120524 | [133] | Biology, NGS | ||
| Kmer | 1934 | [134] | Biology, NGS | ||
| LAMMPS | 28Oct12, 30Sep13 | [135] | Molecular Dynamics Simulation | ||
| Last | 193, 247 | [136] | Biology, Sequence alignment | ||
| Lastz | 1.03.02, 1.02.00 | [137] | Biology, NGS | ||
| LIBSVM | 3.12 | [138] | Machine Learning | ||
| LSC | 0.3, 0.3.1 | [139] | Biology, NGS, Error correction | ||
| Loci | 3.3 | [140] | Fluid Dynamics | ||
| LS-DYNA | 700, 711 | [141] | Physics | ||
| MACH | 1.0.18 | [142] | Biology, Genomics | ||
| MACS | 1.4.2 | [143] | Biology, ChIP-Seq | ||
| mafft | 7.037, 6.903 | [144] | Biology, Multiple sequence alignment | ||
| Maker | 2.10, 2.25b | [145] | Biology, Annotation, Genomics | ||
| Maq | 0.7.1 | [146] | Biology, NGS | ||
| Matlab | 2012a, 2013a, 2014a | [147] | Math, Simulation, Programming | ||
| MATS | 2.1.0, 3.0.6b, 3.0.8 | [148] | BIology, NGS | ||
| MCarts | 1.0 | [149] | Biology, Genomics, Markov models | ||
| MCL | 11-335 | [150] | Biology, Genomics, Clustering | X | |
| MCNP | 5, 6b2 | [151] | Physics | ||
| MCNPX | 2.7.0, 2.7.0-i8 | [152] | Physics | ||
| Meme | 4.8.1 | [153] | Biology, Motifs, Sequence analysis | ||
| Mercurial | 2.7 | [154] | Development, Revision Control | ||
| Metabin | 1.0 | [155] | Biology, Metagenomics | ||
| MetaCluster | 5.0beta | [156] | Biology, Metagenomics | ||
| MetaVelvet | 1.2.01 | [157] | Biology, NGS | ||
| MetaGeneMark | 2012.04 | [158] | Biology, Genomics | ||
| Mfold | 3.6 | [159] | Biology, Genomics | ||
| Midnight Commander | 4.6.1 | [160] | Tools, Utilities | ||
| Migrate-n | 3.3.0 | [161] | Biology, Population | ||
| mira | 3.2.0, 3.4.0.1, 3.9.9, 3.9.18, 4.0.rc1 | [162] | Biology, NGS | ||
| MISO | 0.4.4, 0.4.9 | [163] | Biology, NGS | ||
| MSMBuilder | 2.5.1 | [164] | Molecular Dynamics | ||
| Molden | 5.0 | [165] | Molecular, electronic structure | ||
| mosaik | 2.1.33 | [166] | Biology,NGS | ||
| Mothur | 1.31.2 | [167] | Biology, Microbial Ecology | ||
| MP-EST | 1.4 | [168] | Biology, Phylogenetics | ||
| mpiP | 3.4.1 | [169] | Parallel Computing | ||
| MrBayes | 3.2.1 | [170] | Biology, Phylogenetics | ||
| MUMmer | 3.23 | [171] | Biology, Genomics | ||
| MUSCLE | 3.8.31 | [172] | Biology, Genomics | ||
| NAMD | 2.9 | [173] | Simulation, Chemistry, Biology | ||
| Nbody | 6 | [174] | Astronomy | ||
| NCBI C++ Toolkit | 12.0.0 | [175] | Biology, C++, Development | ||
| NCL | 6.1.2 | [176] | Atmosphere Science | ||
| NCO | 4.2.1, 4.4.3 | [177] | Data exchange tools | ||
| NetCDF | 4.2 | [178] | Data exchange, Tools | ||
| Newbler | 2.6, 2.7 | [179] | Biology, NGS | ||
| Nexus NCL | 2.1.18 | [180] | Biology, Phylogenetics, Library | ||
| NMRPipe | 7.9 | [181] | Biology, Biochemistry | ||
| Novoalign | 2.08.02, 3.00.02 | [182] | Biology, NGS | ||
| Oases | 0.2.08 | [183] | Biology, NGS | ||
| Olego | 1.1.2, 1.1.5 | [184] | Biology, NGS, RNA-Seq | ||
| Octave | 3.6.4 | [185] | Numerical Computation | ||
| OpenBabel | 2.3.2 | [186] | Biology, Chemistry | ||
| OpenCV | 2.4.8 | [187] | Computervision | ||
| OpenFOAM | 2.1.1 | [188] | Fluid Dynamics | ||
| OrthoMCL | 2.0.2, 2.0.3, 2.0.7 | [189] | Biology, Genomics | ||
| PAML | 4.7 | [190] | Biology, Phylogenetics | ||
| ParaView | 4.1.0 | [191] | Data Analysis | ||
| PartitionFinder | 1.0.1, 1.1.1 | [192] | Biology, Phylogenetics, Evolution | ||
| Parflow | v615 | [193] | Ecology, Modeling | ||
| PASA | 1.5, 2.0-r20130605p1, 2.0-r20130907 | [194] | Biology, Genomics | ||
| PeakSplitter | 1.0 | [195] | Biology, Chip-Seq | ||
| PDT | 3.18 | [196] | Programming, Profiler | ||
| Perl | 5.16.0 | [197] | Programming, Language | ||
| PerM | 0.4.0 | [198] | Biology, NGS | ||
| PETSc | 2.3, 3.3 | [199] | Math, Numerical solvers | ||
| Phenix | 1.8.1069 | [200] | Crystallography | ||
| PHITS | 2.52 | [201] | Physics | ||
| PhyloBayes | 3.3f, 1.4f MPI | [202] | Biology, Phylogenetics | ||
| PhyML | 3.0, 20121109 | [203] | Biology, Phylogenetics | ||
| Picard | 1.69, 1.72, 1.80 | [204] | Biology, NGS | ||
| Preseq | 0.0.4 | [205] | Biology, NGS | ||
| ProBABEL | 0.4.2 | [206] | Biology, Genomics, GWAS | ||
| Proteinortho | 4.26 | [207] | Biology, Genomics | ||
| python | 2.6.8, 2.7.3 | [208] | Programming, scripting, language | ||
| QIIME | 1.5.0 | [209] | Biology, Ecology | ||
| QT | 4.8.3 | [210] | Computer Science | ||
| Quickquartet | 1.0.0 | [211] | Biology, Phylogenetics | ||
| R | 2.15.1, 2.15.0-mpi, Rmpi/2.15.1, 3.0.0 | [212] | Statistics, Programming | ||
| R8S | 1.71 | [213] | Biology, Evolution | ||
| RADICAL | 0.2 | [214] | Biology, Phylogenetics, Genomics | ||
| RAxML | 7.9.1, 8.0.0, 8.0.25 | [215] | Biology, Phylogenetics | ||
| RepeatMasker | 3.3.0 | [216] | Biology, Genomics | ||
| Reptile | 1.1 | [217] | Biology, NGS, error correction | ||
| riboPicker | 0.4.3 | [218] | Biology, Sequence | ||
| RNAhybrid | 2.1.1 | [219] | Biology, Genomics | ||
| ROOT | 6.0 | [220] | Data Analysis | ||
| RSEG | 0.4.8 | [221] | Biology, NGS | ||
| Sailfish | 0.6.3 | [222] | Biology, NGS, RNA-Seq | ||
| samtools | 0.1.16, 0.1.18, 0.1.19 | [223] | Biology, NGS | ||
| SAS | 9.3 | [224] | Statistics, Graphing | ||
| SATe | 2.2.7 | [225] | Biology, Phylogenetics | ||
| Sharcgs | 1.2.11 | [226] | Biology, NGS, de novo assembly | ||
| Schrodinger | 2012, 2013 | [227] | Simulation, chemistry | ||
| SCons | 2.3.0 | [228] | Programming, Build System | ||
| SeqPrep | 0.5 | [229] | Biology, NGS | ||
| SEQuel | 1.0.1 | [230] | Biology, NGS | ||
| SeqyClean | 1.8.10 | [231] | Biology, NGS, quality filter | ||
| Sickle | 1.200 | [232] | Biology, NGS, quality filter | ||
| Siesta | 2.0.2,3.1 | [233] | Simulation, Physics, Ab Initio | ||
| SIFT | 4.0.3b | [234] | Biology, Genomics | ||
| Silo | 4.7 | [235] | Library, Data | ||
| Snap | 20100728 | [236] | Biology, Genomics | ||
| SOAPdenovo | 1.05 | [237] | Biology, NGS | ||
| SOAPdenovo-Trans | 1.01, 1.03 | [238] | Biology, NGS | ||
| SparCC | 201402 | [239] | Microbial Ecology | ||
| Spades | 2.5.0, 2.5.1, 3.0.0 | [240] | Biology, NGS | ||
| Spanki | 0.4.1, 0.4.3 | [241] | Biology, NGS, RNA-Seq | ||
| SPARTA+ | 2.60 | [242] | Chemistry | ||
| SPIMAP | 1.1 | [243] | Biology, Phylogenetics | ||
| SpliceTrap | 0.90.5 | [244] | Biology, NGS, RNA-Seq | ||
| SPM | 8 | [245] | Biology, Statistics, Neurology, Imaging | ||
| Sputnik | 1.0 | [246] | Biology, Genomics | ||
| SRA | 2.1.10 | [247]] | biology, NGS | ||
| SSPACE | 2.0 | [248] | Biology, NGS | ||
| Stacks | 0.9995 | [249] | Biology, Genomics, NGS | ||
| STAR | 2.3.0e | [250] | Biology, NGS, Alignment | ||
| STAR-CCM+ | 8.06 | [251] | Mechanical Engineering | ||
| Stata | 10.1, 13 | [252] | Statistics, Data analysis | ||
| Stringtie | 0.97 | [253] | Biology, NGS, Alignment | ||
| Structure | 2.3.3, 2.3.4 | [254] | Biology, Population | ||
| SUNDIALS | 2.3.0, 2.5.0 | [255] | Numerical Solver | ||
| swak4Foam | 2.x | [256] | Fluid Dynamics | ||
| Swig | 2.0.9 | [257] | Programming, C, C++, Python | ||
| Syzygy | 1.2.7 | [258] | Biology, Genomics | ||
| TAU | 2.21.4, 2.23 | [259] | Profiling, Tracing, Programming | ||
| T-Coffee | 9.03.r1318 | [260] | Biology, Genomics, Multiple Alignment | ||
| tgicl | 2.1 | [261] | Biology, sequencing, clustering | ||
| Tophat | 1.4.1, 2.0.1, 2.0.8b | [262] | Biology, NGS | ||
| Totalview | 8.12.0 | [263] | Computer Science | ||
| TPP | 4.7.0 | [264] | Bioinformatics, MassSpec | ||
| TreeFix | 1.1.7 | [265] | Biology, Phylogenetics | ||
| TRF | 4.04 | [266] | Biology, Genomics | ||
| Trilinos | 11.4.1, 11.8.1 | [267] | Math Algorithm | ||
| Trimmomatic | 0.22, 0.32 | [268] | Biology, NGS | ||
| Trinity | r20131110, r20140413 | [269] | Biology, NGS, RNA-Seq | ||
| Twinscan | 4.1.2 | [270] | Biology, Genomics | ||
| usearch | 5.2.32, 7.0.959, 7.0.1001-64 (licensed 64-bit) | [271] | Biology, Sequence analysis | ||
| Valgrind | 3.9.0 | [272] | Computer Science | ||
| VASP | 4.6.34, 5.2.12, 5.3.2, 5.3.3 | [273] | Quantum Chemistry, Ab Initio | ||
| VCFtools | 0.1.9, 0.1.10 | [274] | Biology, SNPs | ||
| velvet | 1.2.06, 1.2.07, 1.2.10 | [275] | Biology, NGS | ||
| vmd | 1.9.1 | [276] | Biology, Visualization | ||
| Wannier90 | 1.2, 2.0.0 | [277] | Computational Physics | ||
| WebLogo | 3.3 | [278] | Biology, Genomics | ||
| WDSSII | 1 | [279] | Meteorology | ||
| WIEN2k | 12.1 | [280] | Material Science, Chemistry | ||
| wgs | 7.0.1.22 | [281] | Biology, NGS | ||
| wublast | 2.0 | [282] | Biology, Sequence Alignment | ||
| Yambo | 3.3.0 | [283] | Physics | ||
| Yasra | 2.32 | [284] | 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.