Difference between revisions of "Installed Software"
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| Line 59: | Line 59: | ||
| [[BamUtil]] || 1.0.2 || [http://genome.sph.umich.edu/wiki/BamUtil] || Biology, NGS | | [[BamUtil]] || 1.0.2 || [http://genome.sph.umich.edu/wiki/BamUtil] || Biology, NGS | ||
|- | |- | ||
| − | | [[BAPS]] || 6.0 || [http://www.helsinki.fi/bsg/software/BAPS/] || Biology | + | | [[BAPS]] || 6.0 || [http://www.helsinki.fi/bsg/software/BAPS/] || Biology, Populaton genetics |
|- | |- | ||
| [[BayesRate]] || 1.3.43 || [http://sourceforge.net/projects/bayesrate/] || Biology, Phylogenetics | | [[BayesRate]] || 1.3.43 || [http://sourceforge.net/projects/bayesrate/] || Biology, Phylogenetics | ||
Revision as of 19:01, 28 May 2015
- Last updated on 2015-05-28.
- Up to three latest versions are listed. The default is shown in bold if it's not the latest version.
- See output of 'module spider module_name' for a full list of provided versions.
A B C D E F G H I J K L M N O P Q R S T U V W X Y
| Name | Version [1] | Website | Category |
|---|---|---|---|
| AbInit | 6.12.3, 7.10.2 | [1] | Quantum Chemistry, DFT |
| Abyss | 1.3.4, 1.3.7, 1.5.2 | [2] | Biology, NGS |
| AFNI | 2011_12_21_1014 | [3] | Biology, Statistics, Imaging, Neurology |
| Agalma | 0.2.1, 0.3.5, 0.5.0 | [4] | Biology, Bioinformatics, Genomics, SNP |
| ALLPATHS-LG | 42316, 44837 | [5] | Biology, NGS |
| Amber | 11, 12, 14 | [6] | Simulation, chemistry |
| AMOS | 3.1.0 | [7] | Biology, Genomics, NGS |
| ANNOVAR | 20130321 | [8] | Biology, Genomics |
| AStalavista | 3.2 | [9] | Biology, NGS, RNA-Seq, Genomics |
| Atlas | 3.10.1, 3.11.17 | [10] | Library, Math |
| Amuse | 6.0 | [11] | Astrophysics |
| ANGSD | 20150306 | [12] | Biology, NGS |
| Affymetrix Power Tools | 1.15.0 | [13] | Biology, Genomics, Microarray |
| ARC | 20140312 | [14] | Biology, NGS |
| Astral | 4.4.4, 4.7.6 | [15] | Biology, Bioinformatics, NGS, Phylogenetics |
| AtomEye | 3 | [16] | Material Science |
| ATRAM | 20140624 | [17] | Biology, NGS |
| Augustus | 2.6 | [18] | Biology, NGS |
| BamBam | 1.0 | [19] | Biology, NGS |
| Bam-readcount | 20150216 | [20] | Biology, NGS |
| Bamstats | 20140602 | [21] | Biology, NGS |
| Bamtools | 2.1.1 | [22] | Biology, NGS |
| BamUtil | 1.0.2 | [23] | Biology, NGS |
| BAPS | 6.0 | [24] | Biology, Populaton genetics |
| BayesRate | 1.3.43 | [25] | Biology, Phylogenetics |
| Bbcp | 12.08.17.00.0 | [26] | Network file transfer |
| Bcbio-nextgen | 0.8.7 | [27] | Biology, NGS |
| Bcftools | 1.0, 1.2 | [28] | Biology, Genomics, NGS |
| Bcl2fastq | 2.16 | [29] | Biology, NGS, Illumina |
| BEAGLE | 3.2.2, 4.0 | [30] | Biology, Genetics, Genotyping |
| BEAST | 1.7.5, 1.8.1, 2.1.3 | [31] | Biology, Phylogenetics |
| Bedops | 2.4.2 | [32] | Biology, Bioinformatics, Sequence, NGS |
| BEDTools | 2.16.2, 2.17.0, 2.23.0 | [33] | Biology, NGS |
| BEST | 2.3 | [34] | Biology, Phylogenetics |
| BETA | 1.0.5 | [35] | Biology, NGS |
| BFAST | 0.7.0 | [36] | Biology, NGS |
| Bismark | 0.7.4, 0.7.7, 0.13.0 | [37] | Biology, NGS, Methylation |
| Bioconductor | Latest | [38] | Biology, R, Statistics |
| BRATNextGen | 20151515 | [39] | Biology, Genomics |
| BioPerl | 1.006901 | [40] | Biology, Perl |
| PHYLDOG | 20130418 | [41] | Biology, Genomics, Phylogenetics |
| Phyluce | c561dd9 | [42] | Biology, Phylogenetics |
| BioPython | 1.59 | [43] | Biology, Python |
| BLASR | 20130815 | [44] | Biology, NGS |
| NCBI BLAST | 2.2.27, 2.2.28, 2.2.29 | [45] | Biology, Sequence alignment |
| Blast2go | 2.5.0-20120705 | [46] | Biology, Annotation |
| BLAT | 20120524 | [47] | Biology, Sequence alignment |
| Blender | 2.63 | [48] | Graphics |
| Boost | 1.49.0, 1.53.0, 1.54.0 | [49] | C++, Library |
| Bowtie | 0.12.9, 1.0.0, 1.1.1 | [50] | Biology, NGS |
| Bowtie2 | 2.2.2, 2.2.3, 2.2.4, 2.2.5 | [51] | Biology, NGS |
| BPP | 2.2, 1.9.0 | [52] | Biology, Phylogenetics |
| BRANCH | 1.8.1 | [53] | Biology, NGS, Mapping |
| Bsmap | 2.74, 2.87 | [54] | Biology, NGS, Methylation |
| Bwa | 0.6.1, 0.7.11, 0.7.12 | [55] | Biology, NGS |
| Camino | 20140723 | [56] | Biology, Neuroscience, Imaging |
| CAP3 | 20120705 | [57] | Biology, sequence assembly |
| CASAVA | 1.8.2 | [58] | Biology, NGS |
| CD-HIT | 4.6 | [59] | Biology, Genomics |
| CDO | 1.6.1 | [60] | Climate |
| CEAS | 1.0.2 | [61] | Biology, Genomics |
| CellProfiler | 2.0 | [62] | Biology, Image Analysis |
| CGATools | 1.6.0.42 | [63] | Biology, NGS |
| Charmm | 36a3 | [64] | Simulation, Chemistry |
| Chartdirector | 5.1.0 | [65] | Graphics |
| Chimera | 1.7 | [66] | Biology, Modeling |
| ChromEvol | 2.0 | [67] | Biology, Phylogenetics |
| CIMS | 4.1.2 | [68] | Biology, Genomics |
| Circos | 0.63-pre11 | [69] | Biology, Visualization |
| CisGenome | 2.0 | [70] | Biology, Genomics, Peak Calling |
| Clann | 3.2.3 | [71] | Biology, Phylogenetics |
| CLHEP | 2.2.0.1 | [72] | High Energy Physics |
| ClonalFrame | 1.1, 1.2 | [73] | Biology, Genomics, NGS |
| ClonalFrameML | 1.25 | [74] | Biology, Genomics, NGS |
| ClustalW | 2.1 | [75] | Biology, Genomics |
| Cluster3 | 1.52 | [76] | Biology, Genomics |
| Clview | 20130402 | [77] | Biology, Genomics |
| ClustalO | 1.2.0 | [78] | Biology, Genomics |
| CMake | 2.8.8, 2.9.12.1, 3.1.0 | [79] | Programming, Build System |
| CNVSeq | 20110715 | [80] | Biology, NGS |
| Coevol | 1.3c, 1.4b | [81] | Biology, Phylogenetics |
| CoMap | 1.4.1 | [82] | Biology, Genomics |
| CONCOCT | 0.3.1 | [83] | Biology, Genomics |
| CoNIFER | 0.2.2 | [84] | Biology, Genomics |
| Consed | 23.0 | [85] | Biology, Genomics |
| Coreutils | 8.23 | [86] | GNU Utilities, Computer Science |
| covNMR | 2014 | [87] | Biochemistry |
| CPLEX | 12.6.5 | [88] | Optimizer |
| CUDA | 4.2, 5.5 | [89] | Programming, Graphics |
| Crux | 1.40 | [90] | Biology, Mass-Spectrometry |
| Cufflinks | 1.3.0, 2.0.2, 2.2.1 | [91] | Biology, NGS |
| Cutadapt | 1.1, 1.7.1 | [92] | Biology, NGS |
| DAKOTA | 5.4.0 | [93] | Computational Science |
| DaPars | 0.9.0 | [94] | Biology, NGS, RNA-Seq |
| DCMTK | 3.6.0 | [95] | Biology, Neuroscience, Imaging |
| DSSAT | 4.5 | [96] | Biology |
| DDSCAT | 7.3.0 | [97] | Astrophysics |
| DDT | 4.1.0, 4.2.1 | [98] | Software |
| Delft3D | 3621 | [99] | Hydrodynamics, Physics |
| Desmond | 3.0.3.1 | [100] | Simulation, Biology, Chemistry |
| DETONATE | 1.9 | [101] | Biology, NGS |
| Dalton | 2011 | [102] | Quantum Chemistry |
| Diamond | 0.5.1 | [103] | Computational Biology, Genomics |
| Dibig Tools | 1.0 | [104] | Bioinformatics, PBS, Torque, Jobs |
| DiffReps | 1.55.4 | [105] | Biology, NGS, ChIP-Seq |
| Dindel | 1.01 | [106] | Biology, NGS |
| DISCOVARdenovo | 52488 | [107] | Biology, NGS |
| DIYABC | 1.0.4.43b, 2.0.3 | [108] | Biology, Genomics |
| Dlpoly | 4.03.4 | [109] | Simulation, Biology, Chemistry |
| DNA Clust | 3.0 | [110] | Biology, Genomics |
| Dock | 6.5, 6.6 | [111] | Chemistry, ligand binding prediction |
| DOT | 2.0 | [112] | Biology, Bioinformatics, Docking |
| Doxygen | 1.8.3.1 | [113] | Programming, Documentation |
| DSSP | 2.2.1 | [114] | Biology, Molecular Dynamics |
| DTI-TK | 2.3.1 | [115] | Biology, Neurology, Imaging |
| EA-Utils | 1.1.2.537 | [116] | Biology, NGS |
| ECTools | 20140311, 20141201 | [117] | Biology, Sequencing, Bioinformatics |
| EEGLAB | 12.0.2.1b, 13.2.2b, 13.4.4b | [118] | Biology, Matlab |
| EIGENSOFT | 4.2, 5.0.1 | [119] | Biology, Population |
| emboss | 6.5.7 | [120] | Biology, multi-tool suite |
| EMIRGE | 20130727 | [121] | Biology, NGS |
| eQTLA | 1.1 | [122] | Biology, Genomics |
| Eqtlbma | 1.2.2 | [123] | Biology, Genotyping |
| Esmf | 6.3.0rp1 | [124] | Climate |
| Espresso | 5.0.1 | [125] | Modeling, Physics |
| ESPRIT | 201211 | [126] | Biology, NGS, Metagenomics |
| ETE2 | 2.1 | [127] | Biology, Phylogenetics |
| Eval | 2.2.8 | [128] | Biology, Genomics, GUI |
| ExaBayes | 1.2.1 | [129] | Biology, Phylogenetics |
| ExaML | 1.0.3, 1.0.5, 1.0.12 | [130] | Biology, Phylogenetics |
| ExomeCNV | 1.4 | [131] | Biology, NGS, Genomics |
| Exonerate | 2.2.0 | [132] | Biology, Genomics |
| eXpress | 1.3.1 | [133] | Biology, NGS |
| FAR | 2.15 | [134] | Biology, Genomics |
| FASTA | 34.26.5, 36.3.6d | [135] | Biology, Genomics |
| FastML | 3.0 | [136] | Biology, Phylogenetics, ML |
| FastQC | 0.9.6, 0.10.1 | [137] | Biology, NGS |
| FastTree | 2.1.7 | [138] | Biology, Phylogenetics |
| Fastx_toolkit | 0.0.13.2 | [139] | Biology, NGS |
| fcGENE | 1.0.7 | [140] | Biology, Genomics, SNP |
| Ferret | 6.82 | [141] | Oceanography, Meteorology |
| FFmpeg | 2.1.3 | [142] | Multimedia, audio, video |
| FFTW | 3.3.2, 3.3.3 | [143] | Math, Library, C++ |
| FLASH | 1.2.10, 1.2.11 | [144] | Biology, Genomics, NGS |
| Flexbar | 2.3 | [145] | Biology, Genomics, NGS |
| Fluent | 14.5.7, 15.0 | [146] | Simulation, Fluid Dynamics |
| FragGeneScan | 1.16 | [147] | Biology, NGS, Genomics |
| FreeBayes | 0.9.6, 0.9.15, 0.9.21 | [148] | Biology, NGS, SNP Calling |
| Freesurfer | 5.2.0 | [149] | Biology, Neurology, Imaging |
| FSL | 5.0.2.2 | [150] | Biology, Neurology, Imaging |
| GapFiller | 1.11 | [151] | Biology, NGS |
| Garli | 2.0, 2.01 | [152] | Biology, Phylogenetics |
| GARM | 0.7.4 | [153] | Biology, NGS |
| GASVPro | 201310 | [154] | Biology, NGS, Genomics |
| GATE | 7.0 | [155] | Data Analysis |
| GATK | 1.6.9, 2.7.4, 3.1.1, 3.3.0 | [156] | Biology, NGS |
| Gaussian | G03, G09-A.02, G09-C.01 | [157] | Modeling, Computational Chemistry |
| Gblocks | 0.91b | [158] | Genomics, Alignment tool |
| Geant4 | 4.10 | [159] | Physics |
| GEM | 20130406 | [160] | Biology, NGS |
| GEMINI | 4.6.6a, 0.13.1 | [161] | Biology, Genomics, Genetics |
| GenBank Tools | 20140130 | [162] | BIology< Genomics |
| GeneMark | 2012.04 | [163] | Biology, Genomics, Metagenomics |
| GeneSeqer | 20140226 | [164] | Biology, Genomics |
| Genewise | 2.2.0 | [165] | Biology, Genomics, Annotation |
| GenomicTools | 2.7.0 | [166] | Biology, NGS |
| GenSel | 4.90 | [167] | Biology, Genetics |
| GKNO | 1.30.18 | [168] | Biology, NGS |
| Git | 1.8.2.1 | [169] | Development, Revision Control |
| Globus | 2.1.3 | [170] | Data Transfer |
| GLPK | 4.55 | [171] | Biology, Genomics |
| Gmap | 20141222 | [172] | Biology, Genomics |
| GNU | 4.4.6, 4.7.2 | [173] | Compilers, Programming |
| GnuPlot | 4.6.0 | [174] | Graphics, Plotting, Programming |
| Grace | 5.1.22 | [175] | Graphics, plotting, 2D |
| GrADS | 2.0.1 | [176] | Earth Science |
| GraphViz | 2.38.0 | [177] | Graphics, plotting, visualization |
| Gromacs | 4.5.5, 4.6.5 | [178] | Chemistry, Modeling, Simulation |
| GSNP | 1.0 | [179] | Biology, Bioinformatics, NGS |
| GSL | 1.15 | [180] | Library, Math, C++, C |
| Gubbins | 20150519 | [181] | Biology, Phylogenetics, Genomics |
| GULP | 4.0 | [182] | Material Science |
| HaMStR | 13.2.2, 13.2.3 | [183] | Biology, Genomics |
| HapCompass | 0.7.7 | [184] | Biology, NGS, Genomics |
| Hapsembler | 2.21 | [185] | Biology, Genomics, NGS |
| HapTree | 1.0 | [186] | Biology, Genomics, NGS |
| HDF4 | 4.2.11 | [187] | Library, Data |
| HDF5 | 1.8.9, 1.8.12 | [188] | Library, Data |
| HMMER3 | 3.0, 3.1b1 | [189] | Biology, Genomics |
| HMMSplicer | 0.9.5 | [190] | Biology, Genomics |
| HOMER | 4.2 | [191] | Biology, Genomics |
| HTMLDoc | 1.2.82 | [192] | Documentation, PDF, HTML |
| HTSeq | 0.5.3p3, 0.6.1p1 | [193] | Biology, NGS |
| HyPhy | 2.1.2.28 | [194] | Biology, Phylogenetics |
| Hypre | 1.10.0b, 2.8.0b | [195] | Library, Math, Physics |
| IDBA-UD | 1.0.9, 1.1.0 | [196] | Biology, NGS |
| IEP | 3.6 | [197] | Programming, Python, Editor |
| iGTP | 1.1 | [198] | Biology, Bioinformatics, Phylogenetics |
| IM and IMa | 20091217 | [199] | Biology, Population |
| IMa2 | 20120827 | [200] | Biology, Population |
| ImageJ | 1.48 | [201] | Image manipulation |
| ImageMagick | 6.8.8-9 | [202] | Image manipulation |
| Intel Compilers | 11.1, 2012 | [203] | Programming, Compilers |
| IOAPI | 3.1 | [204] | Meteorology |
| Iprscan | 4.8 | [205] | Biology, Genomics |
| ITK | 4.3.1 | [206] | Biology, Genomics |
| ITK-SNAP | 3.0.0 | [207] | Biology, Neuroscience, Imaging |
| JAGS | 3.3.0 | [208] | Statistics |
| Java | 1.6.0_31, 1.7.0_02, 1.8.0_31 | [209] | Java Development Kit |
| Jellyfish | 2.1.1 | [210] | Biology, NGS |
| JModelTest | 2.1.1. | [211] | Biology, Phylogenetics, Genomics |
| KaKs | 1.2 | [212] | Biology, Phylogenetics |
| Kent | 20120524 | [213] | Biology, NGS |
| Khmer | 1.1 | [214] | Biology, NGS |
| KING | 1.4 | [215] | Biology, Genomics |
| Kmer | 1934 | [216] | Biology, NGS |
| KmerGenie | 1.6741 | [217] | Biology, NGS, Utilities |
| Kraken | 0.10.4b | [218] | Biology, Genomics, Phylogenetics |
| LAMMPS | 28Oct12, 30Sep13, 28Jun14 | [219] | Molecular Dynamics Simulation |
| LAMP | 2.5 | [220] | Biology, Genomics |
| Last | 193, 247 | [221] | Biology, Sequence alignment |
| Lastz | 1.03.02, 1.02.00 | [222] | Biology, NGS |
| LIBSVM | 3.12 | [223] | Machine Learning |
| LSC | 0.3, 0.3.1 | [224] | Biology, NGS, Error correction |
| Loci | 3.3 | [225] | Fluid Dynamics |
| LS-DYNA | 700, 711 | [226] | Physics |
| Lumpy | 0.2.1 | [227] | Biology, SNP |
| LZO | 2.09 | [228] | Library, Data Compression |
| MACH | 1.0.18 | [229] | Biology, Genomics |
| M5tools | 20121126 | [230] | Biology, Bioinformatics, Genomics |
| MACS | 1.4.2 | [231] | Biology, ChIP-Seq |
| mafft | 7.037, 6.903, 7.215 | [232] | Biology, Multiple sequence alignment |
| Maker | 2.10, 2.25b | [233] | Biology, Annotation, Genomics |
| MapSplice | 2.1.7 | [234] | Biology, NGS, RNA-Seq |
| Maq | 0.7.1 | [235] | Biology, NGS |
| MARK | 2.0.1 | [236] | Statistics |
| MarkerMiner | 20150429, 20150511 | [237] | Biology, Genomics |
| MaSuRCA | 2.3.2 | [238] | Biology, NGS |
| Matlab | 2012a, 2013a, 2014a | [239] | Math, Simulation, Programming |
| MATS | 2.1.0, 3.0.6b, 3.0.8, 3.0.9 | [240] | BIology, NGS |
| Mauve | 2.3.1 | [241] | Biology, NGS |
| MCarts | 1.0.2 | [242] | Biology, Genomics, Markov models |
| MCNP | 5, 6b2 | [243] | Physics |
| MCNPX | 2.7.0, 2.7.0-i8 | [244] | Physics |
| MEGAN | 5.10.3 | [245] | Biology, NGS |
| Melting | 4.3.1 | [246] | Biology, Genome, RNA, Folding |
| Meme | 4.8.1 | [247] | Biology, Motifs, Sequence analysis |
| Mercurial | 2.7 | [248] | Development, Revision Control |
| Metabin | 1.0 | [249] | Biology, Metagenomics |
| MetaCluster | 5.0beta | [250] | Biology, Metagenomics |
| MetaCV | 2.3.0 | [251] | Biology, NGS |
| METAL | 20110325 | [252] | Biology, Genomics |
| MetAMOS | 1.5.0rc4-20140827 | [253] | Biology, Bioinformatics, Genomics, Assembly |
| MetaVelvet | 1.2.01 | [254] | Biology, NGS |
| MetaGeneMark | 2012.04 | [255] | Biology, Genomics |
| Mfold | 3.6 | [256] | Biology, Genomics |
| MIA | 20130301 | [257] | Biology, NGS |
| Midnight Commander | 4.6.1 | [258] | Tools, Utilities |
| Migrate-n | 3.3.0, 3.6.6 | [259] | Biology, Population |
| mira | 3.9.9, 3.9.18, 4.0.rc1 | [260] | Biology, NGS |
| MISO | 0.4.4, 0.4.9, 0.5.2, 0.5.3 | [261] | Biology, NGS |
| MMSEQ | 1.0.8 | [262] | Biology, NGS |
| MSMBuilder | 2.5.1 | [263] | Molecular Dynamics |
| MOABS | 1.2.9 | [264] | Biology, NGS, Genomics |
| Modeller | 9.11, 9.13, 9.14 | [265] | Biology, Modeling |
| Molden | 5.0 | [266] | Molecular, electronic structure |
| MolPro | 2012.1p22 | [267] | Quantum Chemistry, Ab Initio |
| mosaik | 2.1.33, 2.2.3 | [268] | Biology,NGS |
| Mothur | 1.31.2 | [269] | Biology, Microbial Ecology |
| MOTU | 1.1 | [270] | Biology, Bioinformatics, Genomics |
| MP-EST | 1.4 | [271] | Biology, Phylogenetics |
| mpiP | 3.4.1 | [272] | Parallel Computing |
| MrBayes | 3.2.1, 3.2.4, 3.2.5 | [273] | Biology, Phylogenetics |
| MRIcron | 201306 | [274] | Biology, MRI, Imaging |
| MUMmer | 3.23 | [275] | Biology, Genomics |
| MUSCLE | 3.8.31 | [276] | Biology, Genomics |
| MZMine | 2.10, 2.14.2 | [277] | Biology, Spectroscopy |
| NAMD | 2.9 | [278] | Simulation, Chemistry, Biology |
| Nbody | 6 | [279] | Astronomy |
| NCBI C++ Toolkit | 12.0.0 | [280] | Biology, C++, Development |
| NCL | 6.1.2 | [281] | Atmosphere Science |
| NCO | 4.2.1, 4.4.3 | [282] | Data exchange tools |
| Ncview | 2.1.2 | [283] | Data visualization |
| NetCDF | 3.4.2, 4.2, 4.3 | [284] | Data exchange, Tools |
| Newbler | 2.6, 2.7 | [285] | Biology, NGS |
| Newick utils | 1.6 | [286] | Biology, Phylogenetics |
| Nextallele | 20140718 | [287] | Biology, Genomics |
| Nexus NCL | 2.1.18 | [288] | Biology, Phylogenetics, Library |
| ngsCAT | 0.1 | [289] | Biology, Bioinformatics, NGS |
| NGSUtils | 20130722, 20150206 | [290] | Biology, NGS |
| Nipype | 0.10.0 | [291] | Biology, Bioinformatics, Neuroscience, Imaging |
| NMRPipe | 7.9 | [292] | Biology, Biochemistry |
| Novoalign | 2.08.02, 3.00.02 | [293] | Biology, NGS |
| NWChem | 6.5 | [294] | Chemistry |
| Oases | 0.2.08 | [295] | Biology, NGS |
| Olego | 1.1.2, 1.1.5 | [296] | Biology, NGS, RNA-Seq |
| Octave | 3.6.4 | [297] | Numerical Computation |
| OpenBabel | 2.3.2 | [298] | Biology, Chemistry |
| OpenCL | 1.1 | [299] | Programming, Library |
| OpenCV | 2.4.8 | [300] | Computervision |
| OpenFOAM | 2.1.1 | [301] | Fluid Dynamics |
| OpenMM | 6.2.0 | [302] | Quantum Chemistry |
| OrthoFinder | 0.2.5 | [303] | Biology, Genomics |
| OrthoMCL | 2.0.2, 2.0.3, 2.0.7 | [304] | Biology, Genomics |
| p4vasp | 0.3.29 | [305] | Molecular, Electronic Structure |
| Pacbio | 2.2.0, 2.3.0 | [306] | Biology, Bioinformatics, NGS |
| PALES | 122 | [307] | Physics |
| PAML | 4.7, 4.8a | [308] | Biology, Phylogenetics |
| Pandaseq | 20140808 | [309] | Biology, Bioinformatics, NGS, Sequencing |
| PAPI | 5.1.0.2 | [310] | Software, Computing |
| Parallel | 20150122 | [311] | Programming, Languages |
| ParaView | 4.1.0, 4.2.0, 4.3.0 | [312] | Data Analysis |
| PartitionFinder | 1.0.1, 1.1.1 | [313] | Biology, Phylogenetics, Evolution |
| Parflow | v615 | [314] | Ecology, Modeling |
| PASA | 1.5, 2.0-r20150209 | [315] | Biology, Genomics |
| PAUP | 4.0b10 | [316] | Biology, Phylogenetics |
| PBJelly | 14.7.14 | [317] | Biology, Bioinformatics |
| pbsdrmaa | 1.0.17 | [318] | Libraries, Torque |
| PeakSplitter | 1.0 | [319] | Biology, Chip-Seq |
| PEAR | 0.9.2, 0.9.6 | [320] | Biology, NGS |
| PDT | 3.18 | [321] | Programming, Profiler |
| Perl | 5.16.0 | [322] | Programming, Language |
| PerM | 0.4.0 | [323] | Biology, NGS |
| PETSc | 2.3, 3.3 | [324] | Math, Numerical solvers |
| Phenix | 1.8.1069 | [325] | Crystallography |
| PfamScan | 1.3 | [326] | Biology, Genomics |
| PHITS | 2.52 | [327] | Physics |
| Phonopy | 1.9.2 | [328] | Chemistry |
| PhyloBayes | 3.3f, 1.4f MPI | [329] | Biology, Phylogenetics |
| Phylosift | 1.1 | [330] | Biology, Genomics, Phylogenetics, Taxonomy |
| PhyML | 3.0, 20121109 | [331] | Biology, Phylogenetics |
| Picard | 1.69, 1.72, 1.80 | [332] | Biology, NGS |
| PLAST | 1.0 | [333] | Biology, Bioinformatics |
| Plink | 1.07 | [334] | Biology, GWAS |
| PLINKSEQ | 0.10 | [335] | Biology, Genomics |
| PluMiST | 1.1 | [336] | Biology, Phylogenetics, Genomics |
| Preseq | 0.0.4 | [337] | Biology, NGS |
| Primer3 | 2.3.4 | [338] | Biology, Genomics |
| Prokka | 1.10 | [339] | Biology, Genomics, Bioinformatics, Assembly |
| ProBABEL | 0.4.2, 0.4.3 | [340] | Biology, Genomics, GWAS |
| Probalign | 1.4 | [341] | Biology, Genomics |
| Proovread | 1.03rcl | [342] | Biology, Genomics, NGS |
| Proteinortho | 4.26 | [343] | Biology, Genomics |
| Python | 2.7.3, 2.7.5, 2.7.6, 2.7.8 | [344] | Biology, Genomics, NGS |
| Python Modules | see page | [345] | Python, Modules |
| QDD | 3.1.2 | [346] | Programming, scripting, language |
| QIIME | 1.5.0 | [347] | Biology, Ecology |
| QT | 4.8.3 | [348] | Computer Science |
| QUAST | 2.3 | [349] | Biology, NGS |
| Quickquartet | 1.0.0 | [350] | Biology, Phylogenetics |
| R | Rmpi/2.15.1, 3.0.2, 3.2.0 | [351] | Statistics, Programming |
| R8S | 1.71, 1.8 | [352] | Biology, Evolution |
| RADICAL | 0.2 | [353] | Biology, Phylogenetics, Genomics |
| RAxML | 7.9.1, 8.0.25, 8.1.12 | [354] | Biology, Phylogenetics |
| RepeatExplorer | 20150506 | [355] | Biology, Genomics |
| RepeatMasker | 3.3.0 | [356] | Biology, Genomics |
| Reptile | 1.1 | [357] | Biology, NGS, error correction |
| riboPicker | 0.4.3 | [358] | Biology, Sequence |
| RNAhybrid | 2.1.1 | [359] | Biology, Genomics |
| ROOT | 6.0 | [360] | Data Analysis |
| Rosetta | 2014wk4 | [361] | Biology, Structure, Modelling |
| RSEG | 0.4.8 | [362] | Biology, NGS |
| RSEM | 1.1.17, 1.2.7, 1.2.19 | [363] | Biology, NGS, RNA-Seq |
| Ruby | 1.9.3-p0 | [364] | Programming, Scripting, Language |
| Sailfish | 0.6.3 | [365] | Biology, NGS, RNA-Seq |
| Sambamba | 0.5.0-dev, 0.5.1 | [366] | Biology, NGS |
| Samstat | 1.08 | [367] | Biology, NGS, Bioinformatics, Sequencing |
| Samblaster | 0.1.14 | [368] | Biology, NGS |
| samtools | 1.0, 1.1, 1.2 | [369] | Biology, NGS |
| SAS | 9.3 | [370] | Statistics, Graphing |
| SATe | 2.2.7 | [371] | Biology, Phylogenetics |
| Scalablast | 2.4.53, 2.11.5 | [372] | Biology, Genomics |
| Scalpel | 0.1.1 | [373] | Biology, NGS |
| Sharcgs | 1.2.11 | [374] | Biology, NGS, Assembly |
| Schrodinger | 2012, 2013 | [375] | Simulation, chemistry |
| SCons | 2.3.0 | [376] | Programming |
| SCRATCH1D | 1.0 | [377] | Biology, Genomics |
| Scythe | 0.991 | [378] | Biology, NGS |
| Segemehl | 0.1.9 | [379] | Biology, NGS, Mapper |
| SeqPrep | 0.5 | [380] | Biology, NGS |
| SeqMap | 1.0.13 | [381] | Biology, NGS |
| Seqtk | 20140729 | [382] | Biology, NGS |
| SEQuel | 1.0.1 | [383] | Biology, NGS |
| SeqyClean | 1.8.10 | [384] | Biology, NGS, Bioinformatics |
| ShoRAH | 20131204 | [385] | Biology, NGS, quality filter |
| SHRiMP | 2.2.3 | [386] | Biology, NGS |
| Sickle | 1.200, 1.33 | [387] | Biology, NGS, quality filter |
| Siesta | 2.0.2,3.1 | [388] | Simulation, Physics, Ab Initio |
| SIFT | 4.0.3b | [389] | Biology, Genomics |
| Silo | 4.7 | [390] | Library, Data |
| SIPeS | 2.0 | [391] | Biology, Bioinformatics, ChIP-Seq |
| Slicer | 4.3.1 | [392] | Biology, Imaging |
| SMALT | 0.7.6 | [393] | Biology, NGS |
| Snap | 20100728 | [394] | Biology, Genomics |
| SnpEff | 3.3h, 4.0e | [395] | Biology, NGS, Genomics |
| SOAPdenovo | 1.05 | [396] | Biology, NGS |
| SOAPdenovo-Trans | 1.01, 1.03 | [397] | Biology, NGS |
| SOAPsplice | 1.10 | [398] | Biology, NGS |
| SparCC | 201402 | [399] | Microbial Ecology |
| Spades | 3.0.0, 3.1.0, 3.5.0 | [400] | Biology, NGS |
| Spanki | 0.4.1, 0.4.3, 0.5.0 | [401] | Biology, NGS, RNA-Seq |
| SPARTA+ | 2.60 | [402] | Chemistry |
| SPIMAP | 1.1 | [403] | Biology, Phylogenetics |
| SpliceTrap | 0.90.5 | [404] | Biology, NGS, RNA-Seq |
| SPM | 8 | [405] | Biology, Statistics, Neurology, Imaging |
| Sputnik | 1.0 | [406] | Biology, Genomics |
| SQLite | 3.8.8.2 | [407] | Database |
| SRA | 2.1.10 | [408] | biology, NGS |
| SSPACE | 2.0 | [409] | Biology, NGS |
| Stacks | 0.9995 | [410] | Biology, Genomics, NGS |
| STAR | 2.3.0e | [411] | Biology, NGS, Alignment |
| STAR-CCM+ | 8.06 | [412] | Mechanical Engineering |
| Stata | 10.1, 13 | [413] | Statistics, Data analysis |
| Stringtie | 0.97 | [414] | Biology, NGS, Alignment |
| Structure | 2.3.3, 2.3.4 | [415] | Biology, Population |
| SUNDIALS | 2.3.0, 2.5.0 | [416] | Numerical Solver |
| SVDetect | 0.8b | [417] | Biology, NGS, SNP |
| swak4Foam | 2.x | [418] | Fluid Dynamics |
| swarm | 1.2.11 | [419] | Data Analysis |
| Swig | 2.0.9 | [420] | Programming, C, C++, Python |
| SwitchSeq | 20140907 | [421] | Biology, NGS |
| Syzygy | 1.2.7 | [422] | Biology, Genomics |
| TASSEL | 5.0 | [423] | Biology, Genomics |
| TAU | 2.21.4, 2.23 | [424] | Profiling, Tracing, Programming |
| T-Coffee | 9.03.r1318 | [425] | Biology, Genomics, Multiple Alignment |
| TESS | 2.3.1 | [426] | Biology, Genomics, Markov |
| tgicl | 2.1 | [427] | Biology, sequencing, clustering |
| TomoPy | 0.0.3 | [428] | Biology, Neuroimaging |
| Tophat | 1.4.1, 2.0.13 | [429] | Biology, NGS |
| Totalview | 8.12.0 | [430] | Computer Science |
| TPP | 4.7.0 | [431] | Bioinformatics, MassSpec |
| TrackTools | 2011 | [432] | Bioinformatics |
| TrackVis | 0.5.2.2 | [433] | Biology, Spectroscopy |
| Tracula | 5.3.2014_05_26 | [434] | Biology, Bioinformatics, Neuroscience, Imaging |
| TraitRate | 1.1 | [435] | Biology, Evolution |
| TransDecoder | 20140704 | [436] | Biology, NGS |
| TreeFix | 1.1.7 | [437] | Biology, Phylogenetics |
| TreePL | 20150305 | [438] | Biology, Phylogenetics |
| TRF | 4.04 | [439] | Biology, Genomics |
| Trilinos | 11.4.1, 11.8.1 | [440] | Math Algorithm |
| Trim Galore | 0.2.8 | [441] | Biology, NGS |
| Trimmomatic | 0.22, 0.32 | [442] | Biology, NGS |
| Trinity | r20150215-2.0.4 | [443] | Biology, NGS, RNA-Seq |
| TRNAscan-SE | 1.23 | [444] | Biology, NGS, Bioinformatics |
| Twinscan | 4.1.2 | [445] | Biology, Genomics |
| usearch | 7.0.1001-64, 8.0.1517 | [446] | Biology, Sequence analysis |
| UDUNITS | 2.2.17 | [447] | Library, Units, Programming |
| UNAFold | 3.8 | [448] | Biology, Genome, RNA, Folding |
| UProC | 1.2.0 | [449] | Biology, Genomics |
| Valgrind | 3.9.0 | [450] | Computer Science |
| VASP | 5.3.2, 5.3.3, 5.3.5 | [451] | Quantum Chemistry, Ab Initio |
| VarScan | 2.3.6 | [452] | Biology, NGS, Genomics |
| VCFLib | 20141119, 20150313 | [453] | Biology, NGS, Genomics |
| VCFtools | 0.1.11, 0.1.12a, 0.1.12b | [454] | Biology, SNPs |
| velvet | 1.2.06, 1.2.07, 1.2.10 | [455] | Biology, Genomics, NGS |
| VEP | 74 | [456] | Biology, NGS |
| Vim | 7.4.5 | [457] | Programming, Scripting, Language |
| vmd | 1.9.1 | [458] | Biology, Visualization |
| VTK | 6.1.0 | [459] | Visualization, Graphics |
| Wannier90 | 1.2, 2.0.0 | [460] | Computational Physics |
| WebLogo | 3.3 | [461] | Biology, Genomics |
| WDSSII | 1 | [462] | Meteorology |
| WIEN2k | 12.1 | [463] | Material Science, Chemistry |
| Wgs or Celera | 8.2, 8.3rc1, 8.3rc1.r4638 | [464] | Biology, NGS |
| wublast | 2.0 | [465] | Biology, Sequence Alignment |
| YAHA | 0.1.82 | [466] | Biology NGS |
| XCrySDen | 1.5.60 | [467] | Computational Material Science |
| Yambo | 3.3.0 | [468] | Physics |
| YASM | 1.3.0 | [469] | Computer Science |
| Yasra | 2.32 | [470] | 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.