Difference between revisions of "Installed Software"
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|- | |- | ||
| [[SEQuel]] || 1.0.1 || [http://bix.ucsd.edu/SEQuel/index.html] || Biology, NGS | | [[SEQuel]] || 1.0.1 || [http://bix.ucsd.edu/SEQuel/index.html] || Biology, NGS | ||
| + | |- | ||
| + | | [[SeqyClean]] || 1.8.10 || [https://bitbucket.org/izhbannikov/seqyclean] || Biology, NGS, quality filter | ||
|- | |- | ||
| [[Sickle]] || 1.200 || [https://github.com/najoshi/sickle] || Biology, NGS, quality filter | | [[Sickle]] || 1.200 || [https://github.com/najoshi/sickle] || Biology, NGS, quality filter | ||
Revision as of 20:30, 13 December 2013
Installed Software List
Last updated 2013-12-13.
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, 2.17.0 | [18] | Biology, NGS |
| BEST | 2.3 | [19] | Biology, Phylogenetics |
| BETA | 1.0.5 | [20] | Biology, NGS |
| BFAST | 0.7.0 | [21] | Biology, NGS |
| Bismark | 0.7.4, 0.7.7 | [22] | Biology, Methylation, NGS |
| Bioconductor | Latest | [23] | Biology, R, Statistics |
| BioPerl | 1.006901 | [24] | Biology, Perl |
| BioPython | 1.59 | [25] | Biology, Python |
| BLASR | 20130815 | [26] | Biology, NGS |
| NCBI BLAST | 2.2.26, 2.2.27, 2.2.28 | [27] | Biology, Sequence alignment |
| Blast2go | 2.5.0-20120705 | [28] | Biology, Annotation |
| BLAT | 20120524 | [29] | Biology, Sequence alignment |
| Boost | 1.49.0, 1.53.0, 1.54.0 | [30] | C++, Library |
| Bwa | 0.6.1, 0.7.2 | [31] | Biology, NGS |
| Bowtie | 0.12.8, 0.12.9, 2.1.0 | [32] | Biology, NGS |
| CAP3 | 20120705 | [33] | Biology, sequence assembly |
| CASAVA | 1.8.2 | [34] | Biology, NGS |
| CD-HIT | 4.6 | [35] | Biology, Genomics |
| CDO | 1.6.1 | [36] | Climate |
| CellProfiler | 2.0 | [37] | Biology, Image Analysis |
| Charmm | 36a3 | [38] | Simulation, Chemistry |
| Circos | 0.63-pre11 | [39] | Biology, Visualization |
| CisGenome | 2.0 | [40] | Biology, Genomics, Peak Calling |
| ClustalW | 2.1 | [41] | Biology, Genomics |
| Clview | 20130402 | [42] | Biology, Genomics |
| CMake | 2.8.8 | [43] | Programming, Build System |
| Consed | 23.0 | [44] | Biology, Genomics |
| CUDA | 4.2, 5.5 | [45] | Programming, Graphics |
| Cufflinks | 1.3.0, 2.0.0, 2.0.2 | [46] | Biology, NGS |
| Cutadapt | 1.1 | [47] | Biology, NGS |
| DDSCAT | 7.3.0 | [48] | Astrophysics |
| Desmond | 3.0.3.1 | [49] | Simulation, Biology, Chemistry |
| Dalton | 2011 | [50] | Quantum Chemistry |
| Dindel | 1.01 | [51] | Biology, NGS |
| DIYABC | many | [52] | Biology, Genomics |
| Dlpoly | 4.03.4 | [53] | Simulation, Biology, Chemistry |
| DNA Clust | 3.0 | [54] | Biology, Genomics |
| Dock | 6.5, 6.6 | [55] | Chemistry, ligand binding prediction |
| DTI-TK | 2.3.1 | [56] | Biology, Neurology, Imaging |
| EIGENSOFT | 4.2, 5.0.1 | [57] | Biology, Population |
| emboss | 6.5.7 | [58] | Biology, multi-tool suite |
| Espresso | 5.0.1 | [59] | Modeling, Physics |
| ESPRIT | 201211 | [60] | Biology, NGS, Metagenomics |
| ETE2 | 2.1 | [61] | Biology, Phylogenetics |
| Eval | 2.2.8 | [62] | Biology, Genomics, GUI |
| ExaML | 20130314 | [63] | Biology, Phylogenetics |
| Exonerate | 2.2.0 | [64] | Biology, Genomics |
| FAR | 2.15 | [65] | Biology, Genomics |
| FASTA | 34.26.5 | [66] | Biology, Genomics |
| FastML | 3.0 | [67] | Biology, Phylogenetics, ML |
| FastQC | 0.9.6, 0.10.1 | [68] | Biology, NGS |
| Fastx_toolkit | 0.0.13.2 | [69] | Biology, NGS |
| Ferret | 6.82 | [70] | Oceanography, Meteorology |
| FFTW | 3.3.2, 3.3.3 | [71] | Math, Library, C++ |
| Fluent | 14.5.7 | [72] | Simulation, Fluid Dynamics |
| FragGeneScan | 1.16 | [73] | Biology, NGS, Genomics |
| FreeBayes | 0.9.6 | [74] | Biology, NGS, SNP Calling |
| FSL | 5.0.2.2 | [75] | Biology, Neurology, Imaging |
| Garli | 2.0 | [76] | Biology, Phylogenetics |
| GATK | 1.6.9, 2.2.15, 2.6.5 | [77] | Biology, NGS |
| Gaussian | E01, G03, G09-A.02, G09-C.01 | [78] | Modeling, Computational Chemistry |
| GEMINI | 4.6.0a | [79] | Biology, Genomics, Genetics |
| GeneMark | 2012.04 | [80] | Biology, Genomics, Metagenomics |
| Genewise | 2.2.0 | [81] | Biology, Genomics, Annotation |
| GenomicTools | 2.7.0 | [82] | Biology, NGS |
| Git | 1.8.2.1 | [83] | Development, Revision Control |
| Gmap | 20120712, 20130331, 20130618 | [84] | Biology, Genomics |
| GnuPlot | 4.6.0 | [85] | Graphics, Plotting, Programming |
| Grace | 5.1.22 | [86] | Graphics, plotting, 2D |
| GrADS | 2.0.1 | [87] | Earth Science |
| Gromacs | 4.5.5 | [88] | Chemistry, Modeling, Simulation |
| GSL | 1.15 | [89] | Library, Math, C++, C |
| GULP | 4.0 | [90] | Material Science |
| HaMStR | v8b | [91] | Biology, Genomics |
| HDF5 | 1.8.9 | [92] | Library, Data |
| HMMER3 | 3.0 | [93] | Biology, Genomics |
| HOMER | 4.2 | [94] | Biology, Genomics |
| HTSeq | 0.5.3p3 | [95] | Biology, NGS |
| HyPhy | 2.1.2.28 | [96] | Biology, Phylogenetics |
| Hypre | 2.8.0b | [97] | Library, Math, Physics |
| IDBA-UD | 1.0.9, 1.1.0 | [98] | Biology, NGS |
| IM and IMa | 20091217 | [99] | Biology, Population |
| IMa2 | 20120827 | [100] | Biology, Population |
| Intel Compilers | 11.1, 2012 | [101] | Programming, Compilers |
| IOAPI | 3.1 | [102] | Meteorology |
| Iprscan | 4.8 | [103] | Biology, Genomics |
| LS-DYNA | 610 | [104] | Physics |
| ITK | 4.3.1 | [105] | Biology, Genomics |
| JAGS | 3.3.0 | [106] | Statistics |
| Java | 1.6.0_31, 1.7.0_02 | [107] | Java Development Kit |
| Kent | 20120524 | [108] | Biology, NGS |
| Kmer | 1934 | [109] | Biology, NGS |
| LAMMPS | 28Oct12, 30Sep13 | [110] | Molecular Dynamics Simulation |
| Last | 193, 247 | [111] | Biology, Sequence alignment |
| Lastz | 1.03.02, 1.02.00 | [112] | Biology, NGS |
| LIBSVM | 3.12 | [113] | Machine Learning |
| LSC | 0.3 | [114] | Biology, NGS, Error correction |
| MACH | 1.0.18 | [115] | Biology, Genomics |
| MACS | 1.4.2 | [116] | Biology, ChIP-Seq |
| mafft | 7.037, 6.903 | [117] | Biology, Multiple sequence alignment |
| Maker | 2.10, 2.25b | [118] | Biology, Annotation, Genomics |
| Maq | 0.7.1 | [119] | Biology, NGS |
| Matlab | 2012a | [120] | Math, Simulation, Programming |
| MATS | 2.1.0, 3.0.6b, 3.0.8 | [121] | BIology, NGS |
| Mauve | 2.3.1 | [122] | Biology, Genomics, Multiple genome alignments |
| MCNP | 5, 6b2 | [123] | Physics |
| MCNPX | 2.7.0, 2.7.0-i8 | [124] | Physics |
| Meme | 4.8.1 | [125] | Biology, Motifs, Sequence analysis |
| Mercurial | 2.7 | [126] | Development, Revision Control |
| Metabin | 1.0 | [127] | Biology, Metagenomics |
| MetaCluster | 5.0beta | [128] | Biology, Metagenomics |
| MetaVelvet | 1.2.01 | [129] | Biology, NGS |
| MetaGeneMark | 2012.04 | [130] | Biology, Genomics |
| Mfold | 3.6 | [131] | Biology, Genomics |
| Midnight Commander | 4.6.1 | [132] | Tools, Utilities |
| Migrate-n | 3.3.0 | [133] | Biology, Population |
| mira | 3.2.0, 3.4.0.1, 3.9.9, 3.9.18, 4.0.rc1 | [134] | Biology, NGS |
| MISO | 0.4.4 | [135] | Biology, NGS |
| MSMBuilder | 2.5.1 | [136] | Molecular Dynamics |
| Molden | 5.0 | [137] | Molecular, electronic structure |
| mosaik | 2.1.33 | [138] | Biology,NGS |
| Mothur | 1.31.2 | [139] | Biology, Microbial Ecology |
| MrBayes | 3.2.1 | [140] | Biology, Phylogenetics |
| MUMmer | 3.23 | [141] | Biology, Genomics |
| MUSCLE | 3.8.31 | [142] | Biology, Genomics |
| NAMD | 2.9 | [143] | Simulation, Chemistry, Biology |
| Nbody | 6 | [144] | Astronomy |
| NCO | 4.2.1 | [145] | Data exchange tools |
| NetCDF | 4.2 | [146] | Data exchange, Tools |
| Newbler | 2.6, 2.7 | [147] | Biology, NGS |
| NMRPipe | 7.9 | [148] | Biology, Biochemistry |
| Novoalign | 2.08.02, 3.00.02 | [149] | Biology, NGS |
| Oases | 0.2.08 | [150] | Biology, NGS |
| Olego | 1.1.2 | [151] | Biology, NGS, RNA-Seq |
| Octave | 3.6.4 | [152] | Numerical Computation |
| OpenBabel | 2.3.2 | [153] | Biology, Chemistry |
| OpenFOAM | 2.1.1 | [154] | Fluid Dynamics |
| OrthoMCL | 2.0.2, 2.0.3, 2.0.7 | [155] | Biology, Genomics |
| PAML | 4.7 | [156] | Biology, Phylogenetics |
| PartitionFinder | 1.0.1 | [157] | Biology, Phylogenetics, Evolution |
| Parflow | v615 | [158] | Ecology, Modeling |
| PASA | 1.5, 2.0-r20130605p1, 2.0-r20130907 | [159] | Biology, Genomics |
| PeakSplitter | 1.0 | [160] | Biology, Chip-Seq |
| PDT | 3.18 | [161] | Programming, Profiler |
| Perl | 5.16.0 | [162] | Programming, Language |
| PerM | 0.4.0 | [163] | Biology, NGS |
| PETSc | 2.3, 3.3 | [164] | Math, Numerical solvers |
| Phenix | 1.8.1069 | [165] | Crystallography |
| PHITS | 2.52 | [166] | Physics |
| PhyloBayes | 3.3f, 1.4f MPI | [167] | Biology, Phylogenetics |
| PhyML | 3.0, 20121109 | [168] | Biology, Phylogenetics |
| Picard | 1.69, 1.72, 1.80 | [169] | Biology, NGS |
| Preseq | 0.0.4 | [170] | Biology, NGS |
| Proteinortho | 4.26 | [171] | Biology, Genomics |
| python | 2.6.8, 2.7.3 | [172] | Programming, scripting, language |
| QIIME | 1.5.0 | [173] | Biology, Ecology |
| QT | 4.8.3 | [174] | Computer Science |
| R | 2.15.1, 2.15.0-mpi, Rmpi/2.15.1, 3.0.0 | [175] | Statistics, Programming |
| R8S | 1.71 | [176] | Biology, Evolution |
| RADICAL | 0.2 | [177] | Biology, Phylogenetics, Genomics |
| RAxML | 7.3.2.0705, 7.9.1, 8.0.0 | [178] | Biology, Phylogenetics |
| RepeatMasker | 3.3.0 | [179] | Biology, Genomics |
| Reptile | 1.1 | [180] | Biology, NGS, error correction |
| riboPicker | 0.4.3 | [181] | Biology, Sequence |
| RSEG | 0.4.8 | [182] | Biology, NGS |
| samtools | 0.1.16, 0.1.18, 0.1.19 | [183] | Biology, NGS |
| SAS | 9.3 | [184] | Statistics, Graphing |
| SATe | 2.2.7 | [185] | Biology, Phylogenetics |
| Sharcgs | 1.2.11 | [186] | Biology, NGS, de novo assembly |
| Schrodinger | 2012, 2013 | [187] | Simulation, chemistry |
| SCons | 2.3.0 | [188] | Programming, Build System |
| SeqPrep | 0.5 | [189] | Biology, NGS |
| SEQuel | 1.0.1 | [190] | Biology, NGS |
| SeqyClean | 1.8.10 | [191] | Biology, NGS, quality filter |
| Sickle | 1.200 | [192] | Biology, NGS, quality filter |
| Siesta | 2.0.2,3.1 | [193] | Simulation, Physics, Ab Initio |
| SIFT | 4.0.3b | [194] | Biology, Genomics |
| Silo | 4.7 | [195] | Library, Data |
| Snap | 20100728 | [196] | Biology, Genomics |
| SOAPdenovo | 1.05 | [197] | Biology, NGS |
| SOAPdenovo-Trans | 1.01 | [198] | Biology, NGS |
| Spades | 2.5.0, 2.5.1 | [199] | Biology, NGS |
| Spanki | 0.4.1 | [200] | Biology, NGS, RNA-Seq |
| SPARTA+ | 2.60 | [201] | Chemistry |
| SPIMAP | 1.1 | [202] | Biology, Phylogenetics |
| SpliceTrap | 0.90.5 | [203] | Biology, NGS, RNA-Seq |
| SPM | 8 | [204] | Biology, Statistics, Neurology, Imaging |
| Sputnik | 1.0 | [205] | Biology, Genomics |
| SRA | 2.1.10 | [206]] | biology, NGS |
| SSPACE | 2.0 | [207] | Biology, NGS |
| Stacks | 0.9995 | [208] | Biology, Genomics, NGS |
| Stata | 10.1 | [209] | Statistics, Data analysis |
| Structure | 2.3.3, 2.3.4 | [210] | Biology, Population |
| SUNDIALS | 2.5.0 | [211] | Numerical Solver |
| swak4Foam | 2.x | [212] | Fluid Dynamics |
| Swig | 2.0.9 | [213] | Programming, C, C++, Python |
| TAU | 2.21.4 | [214] | Profiling, Tracing, Programming |
| T-Coffee | 9.03.r1318 | [215] | Biology, Genomics, Multiple Alignment |
| tgicl | 2.1 | [216] | Biology, sequencing, clustering |
| Tophat | 1.4.1, 2.0.1, 2.0.8b | [217] | Biology, NGS |
| TreeFix | 1.1.7 | [218] | Biology, Phylogenetics |
| TRF | 4.04 | [219] | Biology, Genomics |
| Trilinos | 11.4.1 | [220] | Math Algorithm |
| Trimmomatic | 0.22 | [221] | Biology, NGS |
| Trinity | r20120905, r20121005, r20120225 | [222] | Biology, NGS, RNA-Seq |
| Twinscan | 4.1.2 | [223] | Biology, Genomics |
| usearch | 5.2.32, 7.0.959, 7.0.1001-64 (licensed 64-bit) | [224] | Biology, Sequence analysis |
| Valgrind | 3.9.0 | [225] | Computer Science |
| VASP | 4.6.34, 5.2.12, 5.3.2, 5.3.3 | [226] | Quantum Chemistry, Ab Initio |
| VCFtools | 0.1.9, 0.1.10 | [227] | Biology, SNPs |
| velvet | 1.2.06, 1.2.07, 1.2.10 | [228] | Biology, NGS |
| vmd | 1.9.1 | [229] | Biology, Visualization |
| WebLogo | 3.3 | [230] | Biology, Genomics |
| WDSSII | 1 | [231] | Meteorology |
| WIEN2k | 12.1 | [232] | Material Science, Chemistry |
| wgs | 7.0.1.22 | [233] | Biology, NGS |
| wublast | 2.0 | [234] | Biology, Sequence Alignment |
| Yambo | 3.3.0 | [235] | Physics |
| Yasra | 2.32 | [236] | 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.