Difference between revisions of "Installed Software"
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| [[arachne]] || 37618 || [http://www.broadinstitute.org/scientific-community/science/programs/genome-sequencing-and-analysis/computational-rd/computational] || Biology, Genomics || X || | | [[arachne]] || 37618 || [http://www.broadinstitute.org/scientific-community/science/programs/genome-sequencing-and-analysis/computational-rd/computational] || Biology, Genomics || X || | ||
|- --> | |- --> | ||
| + | | [[Atlas]] || 3.10.1, 3.11.17 || [http://www.gnu.org/software/gsl] || Library, Math | ||
| + | |- | ||
| [[Amuse]] || 6.0 || [http://www.amusecode.org]|| Astrophysics | | [[Amuse]] || 6.0 || [http://www.amusecode.org]|| Astrophysics | ||
|- | |- | ||
Revision as of 19:59, 6 August 2014
Installed Software List
Last updated 2014-08-06.
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 |
| Boost | 1.49.0, 1.53.0, 1.54.0 | [35] | C++, Library |
| Bwa | 0.6.1, 0.7.9a, 0.7.10 | [36] | Biology, NGS |
| 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 |
| Camino | 20140723 | [39] | Biology, Neuroscience, Imaging |
| CAP3 | 20120705 | [40] | Biology, sequence assembly |
| CASAVA | 1.8.2 | [41] | Biology, NGS |
| CD-HIT | 4.6 | [42] | Biology, Genomics |
| CDO | 1.6.1 | [43] | Climate |
| CEAS | 1.0.2 | [44] | Biology, Genomics |
| CellProfiler | 2.0 | [45] | Biology, Image Analysis |
| Charmm | 36a3 | [46] | Simulation, Chemistry |
| Circos | 0.63-pre11 | [47] | Biology, Visualization |
| CisGenome | 2.0 | [48] | Biology, Genomics, Peak Calling |
| CLHEP | 2.2.0.1 | [49] | High Energy Physics |
| ClustalW | 2.1 | [50] | Biology, Genomics |
| Clview | 20130402 | [51] | Biology, Genomics |
| CMake | 2.8.8 | [52] | Programming, Build System |
| CoMap | 1.4.1 | [53] | Biology, Genomics |
| CONCOCT | 0.3.1 | [54] | Biology, Genomics |
| Consed | 23.0 | [55] | Biology, Genomics |
| covNMR | 2014 | [56] | Biochemistry |
| CUDA | 4.2, 5.5 | [57] | Programming, Graphics |
| Cufflinks | 1.3.0, 2.0.2, 2.2.1 | [58] | Biology, NGS |
| Cutadapt | 1.1 | [59] | Biology, NGS |
| DAKOTA | 5.4.0 | [60] | Computational Science |
| DDSCAT | 7.3.0 | [61] | Astrophysics |
| Delft3D | 3621 | [62] | Hydrodynamics, Physics |
| Desmond | 3.0.3.1 | [63] | Simulation, Biology, Chemistry |
| Dalton | 2011 | [64] | Quantum Chemistry |
| DiffReps | 1.55.4 | [65] | Biology, NGS, ChIP-Seq |
| Dindel | 1.01 | [66] | Biology, NGS |
| DIYABC | many | [67] | Biology, Genomics |
| Dlpoly | 4.03.4 | [68] | Simulation, Biology, Chemistry |
| DNA Clust | 3.0 | [69] | Biology, Genomics |
| Dock | 6.5, 6.6 | [70] | Chemistry, ligand binding prediction |
| DSSP | 2.2.1 | [71] | Biology, Molecular Dynamics |
| DTI-TK | 2.3.1 | [72] | Biology, Neurology, Imaging |
| EA-Utils | 1.1.2.537 | [73] | Biology, NGS |
| EIGENSOFT | 4.2, 5.0.1 | [74] | Biology, Population |
| emboss | 6.5.7 | [75] | Biology, multi-tool suite |
| eQTLA | 1.1 | [76] | Biology, Genomics |
| Espresso | 5.0.1 | [77] | Modeling, Physics |
| ESPRIT | 201211 | [78] | Biology, NGS, Metagenomics |
| ETE2 | 2.1 | [79] | Biology, Phylogenetics |
| Eval | 2.2.8 | [80] | Biology, Genomics, GUI |
| ExaML | 1.0.3, 1.0.5, 1.0.12 | [81] | Biology, Phylogenetics |
| Exonerate | 2.2.0 | [82] | Biology, Genomics |
| FAR | 2.15 | [83] | Biology, Genomics |
| FASTA | 34.26.5, 36.3.6d | [84] | Biology, Genomics |
| FastML | 3.0 | [85] | Biology, Phylogenetics, ML |
| FastQC | 0.9.6, 0.10.1 | [86] | Biology, NGS |
| FastTree | 2.1.7 | [87] | Biology, Phylogenetics |
| Fastx_toolkit | 0.0.13.2 | [88] | Biology, NGS |
| fcGENE | 1.0.7 | [89] | Biology, Genomics, SNP |
| Ferret | 6.82 | [90] | Oceanography, Meteorology |
| FFmpeg | 2.1.3 | [91] | Multimedia, audio, video |
| FFTW | 3.3.2, 3.3.3 | [92] | Math, Library, C++ |
| FLASH | 1.2.10 | [93] | Biology, Genomics, NGS |
| Fluent | 14.5.7, 15.0 | [94] | Simulation, Fluid Dynamics |
| FragGeneScan | 1.16 | [95] | Biology, NGS, Genomics |
| FreeBayes | 0.9.6 | [96] | Biology, NGS, SNP Calling |
| Freesurfer | 5.2.0 | [97] | Biology, Neurology, Imaging |
| FSL | 5.0.2.2 | [98] | Biology, Neurology, Imaging |
| Garli | 2.0, 2.01 | [99] | Biology, Phylogenetics |
| GASVPro | 201310 | [100] | Biology, NGS, Genomics |
| GATE | 7.0 | [101] | Data Analysis |
| GATK | 1.6.9, 2.7.4, 3.1.1 | [102] | Biology, NGS |
| Gaussian | E01, G03, G09-A.02, G09-C.01 | [103] | Modeling, Computational Chemistry |
| Geant4 | 4.10 | [104] | Physics |
| GEM | 20130406 | [105] | Biology, NGS |
| GEMINI | 4.6.6a | [106] | Biology, Genomics, Genetics |
| GenBank Tools | 20140130 | [107] | BIology< Genomics |
| GeneMark | 2012.04 | [108] | Biology, Genomics, Metagenomics |
| Genewise | 2.2.0 | [109] | Biology, Genomics, Annotation |
| GenomicTools | 2.7.0 | [110] | Biology, NGS |
| Git | 1.8.2.1 | [111] | Development, Revision Control |
| Gmap | 20130618, 20130720, 20140530 | [112] | Biology, Genomics |
| GnuPlot | 4.6.0 | [113] | Graphics, Plotting, Programming |
| Grace | 5.1.22 | [114] | Graphics, plotting, 2D |
| GrADS | 2.0.1 | [115] | Earth Science |
| GraphViz | 2.38.0 | [116] | Graphics, plotting, visualization |
| Gromacs | 4.5.5, 4.6.5 | [117] | Chemistry, Modeling, Simulation |
| GSL | 1.15 | [118] | Library, Math, C++, C |
| GULP | 4.0 | [119] | Material Science |
| HaMStR | v8b | [120] | Biology, Genomics |
| Hapsembler | 2.21 | [121] | Biology, Genomics, NGS |
| HDF5 | 1.8.9, 1.8.12 | [122] | Library, Data |
| HMMER3 | 3.0 | [123] | Biology, Genomics |
| HMMSplicer | 0.9.5 | [124] | Biology, Genomics |
| HOMER | 4.2 | [125] | Biology, Genomics |
| HTSeq | 0.5.3p3, 0.6.1p1 | [126] | Biology, NGS |
| HyPhy | 2.1.2.28 | [127] | Biology, Phylogenetics |
| Hypre | 1.10.0b, 2.8.0b | [128] | Library, Math, Physics |
| IDBA-UD | 1.0.9, 1.1.0 | [129] | Biology, NGS |
| IM and IMa | 20091217 | [130] | Biology, Population |
| IMa2 | 20120827 | [131] | Biology, Population |
| ImageMagick | 6.8.8-9 | [132] | Image manipulation |
| Intel Compilers | 11.1, 2012 | [133] | Programming, Compilers |
| IOAPI | 3.1 | [134] | Meteorology |
| Iprscan | 4.8 | [135] | Biology, Genomics |
| ITK | 4.3.1 | [136] | Biology, Genomics |
| ITK-SNAP | 3.0.0 | [137] | Biology, Neuroscience, Imaging |
| JAGS | 3.3.0 | [138] | Statistics |
| Java | 1.6.0_31, 1.7.0_02 | [139] | Java Development Kit |
| Kent | 20120524 | [140] | Biology, NGS |
| Kmer | 1934 | [141] | Biology, NGS |
| LAMMPS | 28Oct12, 30Sep13 | [142] | Molecular Dynamics Simulation |
| Last | 193, 247 | [143] | Biology, Sequence alignment |
| Lastz | 1.03.02, 1.02.00 | [144] | Biology, NGS |
| LIBSVM | 3.12 | [145] | Machine Learning |
| LSC | 0.3, 0.3.1 | [146] | Biology, NGS, Error correction |
| Loci | 3.3 | [147] | Fluid Dynamics |
| LS-DYNA | 700, 711 | [148] | Physics |
| MACH | 1.0.18 | [149] | Biology, Genomics |
| MACS | 1.4.2 | [150] | Biology, ChIP-Seq |
| mafft | 7.037, 6.903 | [151] | Biology, Multiple sequence alignment |
| Maker | 2.10, 2.25b | [152] | Biology, Annotation, Genomics |
| Maq | 0.7.1 | [153] | Biology, NGS |
| Matlab | 2012a, 2013a, 2014a | [154] | Math, Simulation, Programming |
| MATS | 2.1.0, 3.0.6b, 3.0.8 | [155] | BIology, NGS |
| MCarts | 1.0.2 | [156] | Biology, Genomics, Markov models |
| MCNP | 5, 6b2 | [157] | Physics |
| MCNPX | 2.7.0, 2.7.0-i8 | [158] | Physics |
| Meme | 4.8.1 | [159] | Biology, Motifs, Sequence analysis |
| Mercurial | 2.7 | [160] | Development, Revision Control |
| Metabin | 1.0 | [161] | Biology, Metagenomics |
| MetaCluster | 5.0beta | [162] | Biology, Metagenomics |
| MetaVelvet | 1.2.01 | [163] | Biology, NGS |
| MetaGeneMark | 2012.04 | [164] | Biology, Genomics |
| Mfold | 3.6 | [165] | Biology, Genomics |
| Midnight Commander | 4.6.1 | [166] | Tools, Utilities |
| Migrate-n | 3.3.0 | [167] | Biology, Population |
| mira | 3.2.0, 3.4.0.1, 3.9.9, 3.9.18, 4.0.rc1 | [168] | Biology, NGS |
| MISO | 0.4.4, 0.4.9 | [169] | Biology, NGS |
| MSMBuilder | 2.5.1 | [170] | Molecular Dynamics |
| Modeller | 9.11, 9.13, 9.14 | [171] | Biology, Modeling |
| Molden | 5.0 | [172] | Molecular, electronic structure |
| mosaik | 2.1.33 | [173] | Biology,NGS |
| Mothur | 1.31.2 | [174] | Biology, Microbial Ecology |
| MP-EST | 1.4 | [175] | Biology, Phylogenetics |
| mpiP | 3.4.1 | [176] | Parallel Computing |
| MrBayes | 3.2.1 | [177] | Biology, Phylogenetics |
| MRIcron | 201306 | [178] | Biology, MRI, Imaging |
| MUMmer | 3.23 | [179] | Biology, Genomics |
| MUSCLE | 3.8.31 | [180] | Biology, Genomics |
| NAMD | 2.9 | [181] | Simulation, Chemistry, Biology |
| Nbody | 6 | [182] | Astronomy |
| NCBI C++ Toolkit | 12.0.0 | [183] | Biology, C++, Development |
| NCL | 6.1.2 | [184] | Atmosphere Science |
| NCO | 4.2.1, 4.4.3 | [185] | Data exchange tools |
| NetCDF | 4.2 | [186] | Data exchange, Tools |
| Newbler | 2.6, 2.7 | [187] | Biology, NGS |
| Nexus NCL | 2.1.18 | [188] | Biology, Phylogenetics, Library |
| NMRPipe | 7.9 | [189] | Biology, Biochemistry |
| Novoalign | 2.08.02, 3.00.02 | [190] | Biology, NGS |
| Oases | 0.2.08 | [191] | Biology, NGS |
| Olego | 1.1.2, 1.1.5 | [192] | Biology, NGS, RNA-Seq |
| Octave | 3.6.4 | [193] | Numerical Computation |
| OpenBabel | 2.3.2 | [194] | Biology, Chemistry |
| OpenCV | 2.4.8 | [195] | Computervision |
| OpenFOAM | 2.1.1 | [196] | Fluid Dynamics |
| OrthoMCL | 2.0.2, 2.0.3, 2.0.7 | [197] | Biology, Genomics |
| PAML | 4.7 | [198] | Biology, Phylogenetics |
| ParaView | 4.1.0 | [199] | Data Analysis |
| PartitionFinder | 1.0.1, 1.1.1 | [200] | Biology, Phylogenetics, Evolution |
| Parflow | v615 | [201] | Ecology, Modeling |
| PASA | 1.5, 2.0-r20130605p1, 2.0-r20130907 | [202] | Biology, Genomics |
| PeakSplitter | 1.0 | [203] | Biology, Chip-Seq |
| PDT | 3.18 | [204] | Programming, Profiler |
| Perl | 5.16.0 | [205] | Programming, Language |
| PerM | 0.4.0 | [206] | Biology, NGS |
| PETSc | 2.3, 3.3 | [207] | Math, Numerical solvers |
| Phenix | 1.8.1069 | [208] | Crystallography |
| PHITS | 2.52 | [209] | Physics |
| PhyloBayes | 3.3f, 1.4f MPI | [210] | Biology, Phylogenetics |
| PhyML | 3.0, 20121109 | [211] | Biology, Phylogenetics |
| Picard | 1.69, 1.72, 1.80 | [212] | Biology, NGS |
| Preseq | 0.0.4 | [213] | Biology, NGS |
| ProBABEL | 0.4.2 | [214] | Biology, Genomics, GWAS |
| Proovread | 1.03rcl | [215] | Biology, Genomics, NGS |
| Proteinortho | 4.26 | [216] | Biology, Genomics |
| python | 2.6.8, 2.7.3 | [217] | Programming, scripting, language |
| QIIME | 1.5.0 | [218] | Biology, Ecology |
| QT | 4.8.3 | [219] | Computer Science |
| Quickquartet | 1.0.0 | [220] | Biology, Phylogenetics |
| R | 2.15.1, 2.15.0-mpi, Rmpi/2.15.1, 3.0.0 | [221] | Statistics, Programming |
| R8S | 1.71 | [222] | Biology, Evolution |
| RADICAL | 0.2 | [223] | Biology, Phylogenetics, Genomics |
| RAxML | 7.9.1, 8.0.0, 8.0.25 | [224] | Biology, Phylogenetics |
| RepeatMasker | 3.3.0 | [225] | Biology, Genomics |
| Reptile | 1.1 | [226] | Biology, NGS, error correction |
| riboPicker | 0.4.3 | [227] | Biology, Sequence |
| RNAhybrid | 2.1.1 | [228] | Biology, Genomics |
| ROOT | 6.0 | [229] | Data Analysis |
| RSEG | 0.4.8 | [230] | Biology, NGS |
| Sailfish | 0.6.3 | [231] | Biology, NGS, RNA-Seq |
| samtools | 0.1.16, 0.1.18, 0.1.19 | [232] | Biology, NGS |
| SAS | 9.3 | [233] | Statistics, Graphing |
| SATe | 2.2.7 | [234] | Biology, Phylogenetics |
| Sharcgs | 1.2.11 | [235] | Biology, NGS, de novo assembly |
| Schrodinger | 2012, 2013 | [236] | Simulation, chemistry |
| SCons | 2.3.0 | [237] | Programming, Build System |
| SeqPrep | 0.5 | [238] | Biology, NGS |
| SEQuel | 1.0.1 | [239] | Biology, NGS |
| Seqtk | 20140729 | [240] | Biology, NGS |
| SeqyClean | 1.8.10 | [241] | Biology, NGS, quality filter |
| Sickle | 1.200 | [242] | Biology, NGS, quality filter |
| Siesta | 2.0.2,3.1 | [243] | Simulation, Physics, Ab Initio |
| SIFT | 4.0.3b | [244] | Biology, Genomics |
| Silo | 4.7 | [245] | Library, Data |
| Slicer | 4.3.1 | [246] | Biology, Imaging |
| SMALT | 0.7.6 | [247] | Biology, NGS |
| Snap | 20100728 | [248] | Biology, Genomics |
| SOAPdenovo | 1.05 | [249] | Biology, NGS |
| SOAPdenovo-Trans | 1.01, 1.03 | [250] | Biology, NGS |
| SparCC | 201402 | [251] | Microbial Ecology |
| Spades | 2.5.0, 2.5.1, 3.0.0 | [252] | Biology, NGS |
| Spanki | 0.4.1, 0.4.3 | [253] | Biology, NGS, RNA-Seq |
| SPARTA+ | 2.60 | [254] | Chemistry |
| SPIMAP | 1.1 | [255] | Biology, Phylogenetics |
| SpliceTrap | 0.90.5 | [256] | Biology, NGS, RNA-Seq |
| SPM | 8 | [257] | Biology, Statistics, Neurology, Imaging |
| Sputnik | 1.0 | [258] | Biology, Genomics |
| SRA | 2.1.10 | [259]] | biology, NGS |
| SSPACE | 2.0 | [260] | Biology, NGS |
| Stacks | 0.9995 | [261] | Biology, Genomics, NGS |
| STAR | 2.3.0e | [262] | Biology, NGS, Alignment |
| STAR-CCM+ | 8.06 | [263] | Mechanical Engineering |
| Stata | 10.1, 13 | [264] | Statistics, Data analysis |
| Stringtie | 0.97 | [265] | Biology, NGS, Alignment |
| Structure | 2.3.3, 2.3.4 | [266] | Biology, Population |
| SUNDIALS | 2.3.0, 2.5.0 | [267] | Numerical Solver |
| swak4Foam | 2.x | [268] | Fluid Dynamics |
| Swig | 2.0.9 | [269] | Programming, C, C++, Python |
| Syzygy | 1.2.7 | [270] | Biology, Genomics |
| TAU | 2.21.4, 2.23 | [271] | Profiling, Tracing, Programming |
| T-Coffee | 9.03.r1318 | [272] | Biology, Genomics, Multiple Alignment |
| TESS | 2.3.1 | [273] | Biology, Genomics, Markov |
| tgicl | 2.1 | [274] | Biology, sequencing, clustering |
| Tophat | 1.4.1, 2.0.1, 2.0.8b | [275] | Biology, NGS |
| Totalview | 8.12.0 | [276] | Computer Science |
| TPP | 4.7.0 | [277] | Bioinformatics, MassSpec |
| TreeFix | 1.1.7 | [278] | Biology, Phylogenetics |
| TRF | 4.04 | [279] | Biology, Genomics |
| Trilinos | 11.4.1, 11.8.1 | [280] | Math Algorithm |
| Trimmomatic | 0.22, 0.32 | [281] | Biology, NGS |
| Trinity | r20131110, r20140413 | [282] | Biology, NGS, RNA-Seq |
| Twinscan | 4.1.2 | [283] | Biology, Genomics |
| usearch | 5.2.32, 7.0.959, 7.0.1001-64 (licensed 64-bit) | [284] | Biology, Sequence analysis |
| Valgrind | 3.9.0 | [285] | Computer Science |
| VASP | 4.6.34, 5.2.12, 5.3.2, 5.3.3 | [286] | Quantum Chemistry, Ab Initio |
| VCFtools | 0.1.9, 0.1.10 | [287] | Biology, SNPs |
| velvet | 1.2.06, 1.2.07, 1.2.10 | [288] | Biology, NGS |
| vmd | 1.9.1 | [289] | Biology, Visualization |
| Wannier90 | 1.2, 2.0.0 | [290] | Computational Physics |
| WebLogo | 3.3 | [291] | Biology, Genomics |
| WDSSII | 1 | [292] | Meteorology |
| WIEN2k | 12.1 | [293] | Material Science, Chemistry |
| wgs | 7.0.1.22 | [294] | Biology, NGS |
| wublast | 2.0 | [295] | Biology, Sequence Alignment |
| Yambo | 3.3.0 | [296] | Physics |
| Yasra | 2.32 | [297] | 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.