Difference between revisions of "Installed Software"
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| [[PQS]] || 3.3-19 ||[http://www.pqs-chem.com/software.php]||Modeling, Chemistry|| X || | | [[PQS]] || 3.3-19 ||[http://www.pqs-chem.com/software.php]||Modeling, Chemistry|| X || | ||
| + | --> | ||
| + | |- | ||
| + | | [[Preseq]] || 0.0.4 || [http://smithlab.usc.edu/plone/software/librarycomplexity] || Biology, NGS || X || | ||
| + | <!-- | ||
|- | |- | ||
| [[Prinseq]] || 0.17 || [http://prinseq.sourceforge.net/index.html] || Biology, NGS || X || | | [[Prinseq]] || 0.17 || [http://prinseq.sourceforge.net/index.html] || Biology, NGS || X || | ||
Revision as of 16:19, 12 November 2013
Installed Software List
Last updated 2013-11-12.
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 | 1.3.3, 1.3.4, 1.3.4-mpi | [2] | Biology, NGS | ||||||
| ALLPATHS-LG | 42316, 44837 | [3] | Biology, NGS | ||||||
| AFNI | 2011_12_21_1014 | [4] | Biology, Statistics, Imaging, Neurology | ||||||
| Amber | 11, 12 | [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 | ||||||
| Augustus | 2.6 | [10] | Biology, NGS | ||||||
| BamBam | 1.0 | [11] | Biology, NGS | ||||||
| Bamtools | 2.1.1 | [12] | Biology, NGS | ||||||
| BamUtil | 1.0.2 | [13] | Biology, NGS | ||||||
| BayesRate | 1.3.43 | [14] | Biology, Phylogenetics | ||||||
| Bbcp | 12.08.17.00.0 | [15] | Network file transfer | ||||||
| BEAGLE | 3.2.2 | [16] | Biology, Genetics, Genotyping | ||||||
| BEAST | 1.7.5, 2.0.1, 2.0.2.pre | [17] | Biology, Phylogenetics | ||||||
| BEDTools | 2.16.2 | [18] | Biology, NGS | ||||||
| BEST | 2.3 | [19] | Biology, Phylogenetics | ||||||
| BFAST | 0.7.0 | [20] | Biology, NGS | ||||||
| Bismark | 0.7.4, 0.7.7 | [21] | Biology, Methylation, NGS | ||||||
| Bioconductor | Latest | [22] | Biology, R, Statistics | ||||||
| BioPerl | 1.006901 | [23] | Biology, Perl | ||||||
| BioPython | 1.59 | [24] | Biology, Python | ||||||
| BLASR | 20130815 | [25] | Biology, NGS | ||||||
| NCBI BLAST | 2.2.26, 2.2.27, 2.2.28 | [26] | Biology, Sequence alignment | ||||||
| Blast2go | 2.5.0-20120705 | [27] | Biology, Annotation | ||||||
| BLAT | 20120524 | [28] | Biology, Sequence alignment | ||||||
| Boost | 1.49.0, 1.53.0, 1.54.0 | [29] | C++, Library | ||||||
| Bwa | 0.6.1, 0.7.2 | [30] | Biology, NGS | ||||||
| Bowtie | 0.12.8, 0.12.9, 2.1.0 | [31] | Biology, NGS | ||||||
| CAP3 | 20120705 | [32] | Biology, sequence assembly | ||||||
| CASAVA | 1.8.2 | [33] | Biology, NGS | ||||||
| CD-HIT | 4.6 | [34] | Biology, Genomics | ||||||
| CDO | 1.6.1 | [35] | Climate | ||||||
| CellProfiler | 2.0 | [36] | Biology, Image Analysis | ||||||
| Charmm | 36a3 | [37] | Simulation, Chemistry | ||||||
| Circos | 0.63-pre11 | [38] | Biology, Visualization | ||||||
| CisGenome | 2.0 | [39] | Biology, Genomics, Peak Calling | ||||||
| ClustalW | 2.1 | [40] | Biology, Genomics | ||||||
| Clview | 20130402 | [41] | Biology, Genomics | ||||||
| CMake | 2.8.8 | [42] | Programming, Build System | ||||||
| Consed | 23.0 | [43] | Biology, Genomics | ||||||
| CUDA | 4.2, 5.5 | [44] | Programming, Graphics | ||||||
| Cufflinks | 1.3.0, 2.0.0, 2.0.2 | [45] | Biology, NGS | ||||||
| Cutadapt | 1.1 | [46] | Biology, NGS | ||||||
| Desmond | 3.0.3.1 | [47] | Simulation, Biology, Chemistry | ||||||
| Dalton | 2011 | [48] | Quantum Chemistry | ||||||
| Dindel | 1.01 | [49] | Biology, NGS | ||||||
| DIYABC | many | [50] | Biology, Genomics | ||||||
| Dlpoly | 4.03.4 | [51] | Simulation, Biology, Chemistry | ||||||
| DNA Clust | 3.0 | [52] | Biology, Genomics | ||||||
| Dock | 6.5, 6.6 | [53] | Chemistry, ligand binding prediction | ||||||
| DTI-TK | 2.3.1 | [54] | Biology, Neurology, Imaging | ||||||
| EIGENSOFT | 4.2, 5.0.1 | [55] | Biology, Population | ||||||
| emboss | 6.5.7 | [56] | Biology, multi-tool suite | ||||||
| Espresso | 5.0.1 | [57] | Modeling, Physics | ||||||
| ESPRIT | 201211 | [58] | Biology, NGS, Metagenomics | ||||||
| ETE2 | 2.1 | [59] | Biology, Phylogenetics | ||||||
| Eval | 2.2.8 | [60] | Biology, Genomics, GUI | ||||||
| ExaML | 20130314 | [61] | Biology, Phylogenetics | ||||||
| Exonerate | 2.2.0 | [62] | Biology, Genomics | ||||||
| FAR | 2.15 | [63] | Biology, Genomics | ||||||
| FASTA | 34.26.5 | [64] | Biology, Genomics | ||||||
| FastML | 3.0 | [65] | Biology, Phylogenetics, ML | ||||||
| FastQC | 0.9.6, 0.10.1 | [66] | Biology, NGS | ||||||
| Fastx_toolkit | 0.0.13.2 | [67] | Biology, NGS | ||||||
| Ferret | 6.82 | [68] | Oceanography, Meteorology | ||||||
| FFTW | 3.3.2, 3.3.3 | [69] | Math, Library, C++ | ||||||
| Fluent | 14.5.7 | [70] | Simulation, Fluid Dynamics | ||||||
| FragGeneScan | 1.16 | [71] | Biology, NGS, Genomics | ||||||
| FreeBayes | 0.9.6 | [72] | Biology, NGS, SNP Calling | ||||||
| FSL | 5.0.2.2 | [73] | Biology, Neurology, Imaging | ||||||
| Garli | 2.0 | [74] | Biology, Phylogenetics | ||||||
| GATK | 1.6.9, 2.2.15, 2.6.5 | [75] | Biology, NGS | ||||||
| Gaussian | E01, G03, G09-A.02, G09-C.01 | [76] | Modeling, Computational Chemistry | ||||||
| GeneMark | 2012.04 | [77] | Biology, Genomics, Metagenomics | ||||||
| Genewise | 2.2.0 | [78] | Biology, Genomics, Annotation | ||||||
| GenomicTools | 2.7.0 | [79] | Biology, NGS | ||||||
| Git | 1.8.2.1 | [80] | Development, Revision Control | ||||||
| Gmap | 20120712, 20130331, 20130618 | [81] | Biology, Genomics | ||||||
| GnuPlot | 4.6.0 | [82] | Graphics, Plotting, Programming | ||||||
| Grace | 5.1.22 | [83] | Graphics, plotting, 2D | ||||||
| GrADS | 2.0.1 | [84] | Earth Science | ||||||
| Gromacs | 4.5.5 | [85] | Chemistry, Modeling, Simulation | ||||||
| GSL | 1.15 | [86] | Library, Math, C++, C | ||||||
| GULP | 4.0 | [87] | Material Science | ||||||
| HaMStR | v8b | [88] | Biology, Genomics | ||||||
| HDF5 | 1.8.9 | [89] | Library, Data | ||||||
| HMMER3 | 3.0 | [90] | Biology, Genomics | ||||||
| HOMER | 4.2 | [91] | Biology, Genomics | ||||||
| HTSeq | 0.5.3p3 | [92] | Biology, NGS | ||||||
| HyPhy | 2.1.2.28 | [93] | Biology, Phylogenetics | ||||||
| Hypre | 2.8.0b | [94] | Library, Math, Physics | ||||||
| IDBA-UD | 1.0.9, 1.1.0 | [95] | Biology, NGS | ||||||
| IM and IMa | 20091217 | [96] | Biology, Population | ||||||
| IMa2 | 20120827 | [97] | Biology, Population | ||||||
| Intel Compilers | 11.1, 2012 | [98] | Programming, Compilers | ||||||
| IOAPI | 3.1 | [99] | Meteorology | ||||||
| Iprscan | 4.8 | [100] | Biology, Genomics | ||||||
| LS-DYNA | 610 | [101] | Physics | ||||||
| ITK | 4.3.1 | [102] | Biology, Genomics | ||||||
| JAGS | 3.3.0 | [103] | Statistics | ||||||
| Java | 1.6.0_31, 1.7.0_02 | [104] | Java Development Kit | ||||||
| Kent | 20120524 | [105] | Biology, NGS | ||||||
| Kmer | 1934 | [106] | Biology, NGS | ||||||
| LAMMPS | 28Oct12, 30Sep13 | [107] | Molecular Dynamics Simulation | ||||||
| Last | 193, 247 | [108] | Biology, Sequence alignment | ||||||
| Lastz | 1.03.02, 1.02.00 | [109] | Biology, NGS | ||||||
| LIBSVM | 3.12 | [110] | Machine Learning | ||||||
| LSC | 0.3 | [111] | Biology, NGS, Error correction | ||||||
| MACS | 1.4.2 | [112] | Biology, ChIP-Seq | ||||||
| mafft | 7.037, 6.903 | [113] | Biology, Multiple sequence alignment | ||||||
| Maker | 2.10, 2.25b | [114] | Biology, Annotation, Genomics | ||||||
| Maq | 0.7.1 | [115] | Biology, NGS | ||||||
| Matlab | 2012a | [116] | Math, Simulation, Programming | ||||||
| MATS | 2.1.0, 3.0.6b, 3.0.8 | [117] | BIology, NGS | ||||||
| Mauve | 2.3.1 | [118] | Biology, Genomics, Multiple genome alignments | ||||||
| MCNP | 5, 6b2 | [119] | Physics | ||||||
| MCNPX | 2.7.0, 2.7.0-i8 | [120] | Physics | ||||||
| Meme | 4.8.1 | [121] | Biology, Motifs, Sequence analysis | ||||||
| Mercurial | 2.7 | [122] | Development, Revision Control | ||||||
| Metabin | 1.0 | [123] | Biology, Metagenomics | ||||||
| MetaCluster | 5.0beta | [124] | Biology, Metagenomics | ||||||
| MetaVelvet | 1.2.01 | [125] | Biology, NGS | ||||||
| MetaGeneMark | 2012.04 | [126] | Biology, Genomics | ||||||
| Mfold | 3.6 | [127] | Biology, Genomics | ||||||
| Midnight Commander | 4.6.1 | [128] | Tools, Utilities | ||||||
| Migrate-n | 3.3.0 | [129] | Biology, Population | ||||||
| mira | 3.2.0, 3.4.0.1, 3.9.9, 3.9.18, 4.0.rc1 | [130] | Biology, NGS | ||||||
| MISO | 0.4.4 | [131] | Biology, NGS | ||||||
| MSMBuilder | 2.5.1 | [132] | Molecular Dynamics | ||||||
| Molden | 5.0 | [133] | Molecular, electronic structure | ||||||
| mosaik | 2.1.33 | [134] | Biology,NGS | ||||||
| Mothur | 1.31.2 | [135] | Biology, Microbial Ecology | ||||||
| MrBayes | 3.2.1 | [136] | Biology, Phylogenetics | ||||||
| MUMmer | 3.23 | [137] | Biology, Genomics | ||||||
| MUSCLE | 3.8.31 | [138] | Biology, Genomics | ||||||
| NAMD | 2.9 | [139] | Simulation, Chemistry, Biology | ||||||
| Nbody | 6 | [140] | Astronomy | ||||||
| NCO | 4.2.1 | [141] | Data exchange tools | ||||||
| NetCDF | 4.2 | [142] | Data exchange, Tools | ||||||
| Newbler | 2.6, 2.7 | [143] | Biology, NGS | ||||||
| NMRPipe | 7.9 | [144] | Biology, Biochemistry | ||||||
| Novoalign | 2.08.02, 3.00.02 | [145] | Biology, NGS | ||||||
| Oases | 0.2.08 | [146] | Biology, NGS | ||||||
| Olego | 1.1.2 | [147] | Biology, NGS, RNA-Seq | ||||||
| Octave | 3.6.4 | [148] | Numerical Computation | ||||||
| OpenBabel | 2.3.2 | [149] | Biology, Chemistry | ||||||
| OpenFOAM | 2.1.1 | [150] | Fluid Dynamics | ||||||
| OrthoMCL | 2.0.2, 2.0.3, 2.0.7 | [151] | Biology, Genomics | ||||||
| PAML | 4.7 | [152] | Biology, Phylogenetics | ||||||
| PartitionFinder | 1.0.1 | [153] | Biology, Phylogenetics, Evolution | ||||||
| Parflow | v615 | [154] | Ecology, Modeling | ||||||
| PASA | 1.5, 2.0-r20130605p1, 2.0-r20130907 | [155] | Biology, Genomics | ||||||
| PeakSplitter | 1.0 | [156] | Biology, Chip-Seq | ||||||
| PDT | 3.18 | [157] | Programming, Profiler | ||||||
| Perl | 5.16.0 | [158] | Programming, Language | ||||||
| PerM | 0.4.0 | [159] | Biology, NGS | ||||||
| PETSc | 2.3, 3.3 | [160] | Math, Numerical solvers | ||||||
| Phenix | 1.8.1069 | [161] | Crystallography | ||||||
| PHITS | 2.52 | [162] | Physics | ||||||
| PhyloBayes | 3.3f, 1.4f MPI | [163] | Biology, Phylogenetics | ||||||
| PhyML | 3.0, 20121109 | [164] | Biology, Phylogenetics | ||||||
| Picard | 1.69, 1.72, 1.80 | [165] | Biology, NGS | ||||||
| Preseq | 0.0.4 | [166] | Biology, NGS | X | Proteinortho | 4.26 | [167] | Biology, Genomics | |
| python | 2.6.8, 2.7.3 | [168] | Programming, scripting, language | ||||||
| QIIME | 1.5.0 | [169] | Biology, Ecology | ||||||
| QT | 4.8.3 | [170] | Computer Science | ||||||
| R | 2.15.1, 2.15.0-mpi, Rmpi/2.15.1, 3.0.0 | [171] | Statistics, Programming | ||||||
| R8S | 1.71 | [172] | Biology, Evolution | ||||||
| RADICAL | 0.2 | [173] | Biology, Phylogenetics, Genomics | ||||||
| RAxML | 7.3.2.0705 | [174] | Biology, Phylogenetics | ||||||
| RepeatMasker | 3.3.0 | [175] | Biology, Genomics | ||||||
| Reptile | 1.1 | [176] | Biology, NGS, error correction | ||||||
| riboPicker | 0.4.3 | [177] | Biology, Sequence | ||||||
| RSEG | 0.4.8 | [178] | Biology, NGS | ||||||
| samtools | 0.1.16, 0.1.18, 0.1.19 | [179] | Biology, NGS | ||||||
| SAS | 9.3 | [180] | Statistics, Graphing | ||||||
| SATe | 2.2.7 | [181] | Biology, Phylogenetics | ||||||
| Sharcgs | 1.2.11 | [182] | Biology, NGS, de novo assembly | ||||||
| Schrodinger | 2012, 2013 | [183] | Simulation, chemistry | ||||||
| SCons | 2.3.0 | [184] | Programming, Build System | ||||||
| SeqPrep | 0.5 | [185] | Biology, NGS | ||||||
| SEQuel | 1.0.1 | [186] | Biology, NGS | ||||||
| Sickle | 1.200 | [187] | Biology, NGS, quality filter | ||||||
| Siesta | 2.0.2,3.1 | [188] | Simulation, Physics, Ab Initio | ||||||
| SIFT | 4.0.3b | [189] | Biology, Genomics | ||||||
| Silo | 4.7 | [190] | Library, Data | ||||||
| Snap | 20100728 | [191] | Biology, Genomics | ||||||
| SOAPdenovo | 1.05 | [192] | Biology, NGS | ||||||
| SOAPdenovo-Trans | 1.01 | [193] | Biology, NGS | ||||||
| Spades | 2.5.0, 2.5.1 | [194] | Biology, NGS | ||||||
| Spanki | 0.4.1 | [195] | Biology, NGS, RNA-Seq | ||||||
| SPARTA+ | 2.60 | [196] | Chemistry | ||||||
| SPIMAP | 1.1 | [197] | Biology, Phylogenetics | ||||||
| SpliceTrap | 0.90.5 | [198] | Biology, NGS, RNA-Seq | ||||||
| SPM | 8 | [199] | Biology, Statistics, Neurology, Imaging | ||||||
| Sputnik | 1.0 | [200] | Biology, Genomics | ||||||
| SRA | 2.1.10 | [201]] | biology, NGS | ||||||
| SSPACE | 2.0 | [202] | Biology, NGS | ||||||
| Stacks | 0.9995 | [203] | Biology, Genomics, NGS | ||||||
| Stata | 10.1 | [204] | Statistics, Data analysis | ||||||
| Structure | 2.3.3, 2.3.4 | [205] | Biology, Population | ||||||
| SUNDIALS | 2.5.0 | [206] | Numerical Solver | ||||||
| swak4Foam | 2.x | [207] | Fluid Dynamics | ||||||
| Swig | 2.0.9 | [208] | Programming, C, C++, Python | ||||||
| TAU | 2.21.4 | [209] | Profiling, Tracing, Programming | ||||||
| T-Coffee | 9.03.r1318 | [210] | Biology, Genomics, Multiple Alignment | ||||||
| tgicl | 2.1 | [211] | Biology, sequencing, clustering | ||||||
| Tophat | 1.4.1, 2.0.1, 2.0.8b | [212] | Biology, NGS | ||||||
| TreeFix | 1.1.7 | [213] | Biology, Phylogenetics | ||||||
| TRF | 4.04 | [214] | Biology, Genomics | ||||||
| Trilinos | 11.4.1 | [215] | Math Algorithm | ||||||
| Trimmomatic | 0.22 | [216] | Biology, NGS | ||||||
| Trinity | r20120905, r20121005, r20120225 | [217] | Biology, NGS, RNA-Seq | ||||||
| Twinscan | 4.1.2 | [218] | Biology, Genomics | ||||||
| usearch | 5.2.32, 7.0.959 | [219] | Biology, Sequence analysis | ||||||
| VASP | 4.6.34, 5.2.12, 5.3.2 | [220] | Quantum Chemistry, Ab Initio | ||||||
| VCFtools | 0.1.9, 0.1.10 | [221] | Biology, SNPs | ||||||
| velvet | 1.2.06, 1.2.07, 1.2.10 | [222] | Biology, NGS | ||||||
| vmd | 1.9.1 | [223] | Biology, Visualization | ||||||
| WebLogo | 3.3 | [224] | Biology, Genomics | ||||||
| WDSSII | 1 | [225] | Meteorology | ||||||
| WIEN2k | 12.1 | [226] | Material Science, Chemistry | ||||||
| wgs | 7.0.1.22 | [227] | Biology, NGS | ||||||
| wublast | 2.0 | [228] | Biology, Sequence Alignment | ||||||
| Yambo | 3.3.0 | [229] | Physics | ||||||
| Yasra | 2.32 | [230] | 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.