Difference between revisions of "Installed Software"
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|- | |- | ||
| [[DDT]] || 4.1.0, 4.2.1 || [http://www.allinea.com/products/ddt] || Software | | [[DDT]] || 4.1.0, 4.2.1 || [http://www.allinea.com/products/ddt] || Software | ||
+ | |- | ||
+ | | [[DealII]] || 8.3.0 || [https://dealii.org/download.html] || Library | ||
|- | |- | ||
| [[Delft3D]] || 3621 || [http://oss.deltares.nl/web/delft3d] || Hydrodynamics, Physics | | [[Delft3D]] || 3621 || [http://oss.deltares.nl/web/delft3d] || Hydrodynamics, Physics |
Revision as of 19:51, 10 January 2016
- Last updated on 2016-01-10.
- 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 |
---|---|---|---|
4P | 1.0 | [1] | Biology, SNP |
AbInit | 6.12.3, 7.10.2, 7.10.4 | [2] | Quantum Chemistry, DFT |
Abyss | 1.3.4, 1.3.7, 1.5.2 | [3] | Biology, NGS |
AdmixTools | 20150311 | [4] | Biology, Bioinformatics, Genomics, NGS |
ADMIXTURE | 1.23 | [5] | Biology, Bioinformatics, Genomics, NGS |
AEGeAn | 0.14.0 | [6] | Biology, Genomics |
AFNI | 2013_05_31, 2013_11_24 | [7] | Biology, Statistics, Imaging, Neurology |
Agalma | 0.2.1, 0.3.5, 0.5.0 | [8] | Biology, Bioinformatics, Genomics, SNP |
ALE | 20150507 | [9] | Biology, Bioinformatics, Assembly |
ALLPATHS-LG | 42316, 44837 | [10] | Biology, NGS |
Amber | 11, 12, 14 | [11] | Simulation, chemistry |
AMOS | 3.1.0 | [12] | Biology, Genomics, NGS |
ANNOVAR | 20120621, 20150322 | [13] | Biology, Genomics |
AStalavista | 3.2 | [14] | Biology, NGS, RNA-Seq, Genomics |
ASTRID | 20150807 | [15] | Biology, Genomics |
Atlas | 3.10.1, 3.11.17 | [16] | Library, Math |
Amuse | 6.0, 10.0 | [17] | Astrophysics |
ANGSD | 20150306, 20150909 | [18] | Biology, NGS |
Affymetrix Power Tools | 1.15.0, 1.18.0 | [19] | Biology, Genomics, Microarray |
ARC | 20140312 | [20] | Biology, NGS |
Armadillo | 6.200.3 | [21] | Library, C++ , Math |
Astral | 4.7.6, 4.7.8, 4.7.9 | [22] | Biology, Bioinformatics, NGS, Phylogenetics |
AtomEye | 3 | [23] | Material Science |
ATRAM | 20140624 | [24] | Biology, NGS |
Augustus | 2.6, 3.2.1 | [25] | Biology, NGS |
Auto3DEM | 4.05.1 | [26] | Image Reconstruction |
BamBam | 1.0 | [27] | Biology, NGS |
Bam-readcount | 20150216 | [28] | Biology, NGS |
Bamstats | 20140602 | [29] | Biology, NGS |
Bamtools | 2.1.1 | [30] | Biology, NGS |
BamUtil | 1.0.2 | [31] | Biology, NGS |
Bam-Readcount | 20150616 | [32]] | Biology, Genomics |
BAPS | 6.0 | [33] | Biology, Populaton genetics |
Basemount | 0.1.2.464 | [34] | Biology, DNA Sequencing |
BayesRate | 1.3.43 | [35] | Biology, Phylogenetics |
Bbcp | 12.08.17.00.0 | [36] | Network file transfer |
Bcbio-nextgen | 0.8.7 | [37] | Biology, NGS |
Bcftools | 1.0, 1.2 | [38] | Biology, Genomics, NGS |
Bcl2fastq | 2.16 | [39] | Biology, NGS, Illumina |
BEAGLE | 3.2.2, 4.0 | [40] | Biology, Genetics, Genotyping |
BEAST | 1.7.5, 1.8.1, 2.1.3 | [41] | Biology, Phylogenetics |
Bedops | 2.4.2 | [42] | Biology, Bioinformatics, Sequence, NGS |
BEDTools | 2.17.0, 2.23.0, 2.24.0 | [43] | Biology, NGS |
BEST | 2.3 | [44] | Biology, Phylogenetics |
BETA | 1.0.5 | [45] | Biology, NGS |
BFAST | 0.7.0 | [46] | Biology, NGS |
Bismark | 0.7.4, 0.7.7, 0.13.0 | [47] | Biology, NGS, Methylation |
Bioconductor | Latest | [48] | Biology, R, Statistics |
BioPerl | 1.006901 | [49] | Biology, Perl |
BioPython | 1.59 | [50] | Biology, Python |
BLASR | 20130815 | [51] | Biology, NGS |
NCBI BLAST | 2.2.27, 2.2.28, 2.2.29 | [52] | Biology, Sequence alignment |
Blast2go | 2.5.0-20120705 | [53] | Biology, Annotation |
BLAT | 20120524 | [54] | Biology, Sequence alignment |
Blender | 2.63 | [55] | Graphics |
Boost | 1.49.0, 1.53.0, 1.54.0 | [56] | C++, Library |
Bowtie | 0.12.9, 1.0.0, 1.1.1 | [57] | Biology, NGS |
Bowtie2 | 2.2.4, 2.2.5, 2.2.6 | [58] | Biology, NGS |
BPP | 1.9.0, 2.2, 3.2 | [59] | Biology, Phylogenetics |
BRANCH | 1.8.1 | [60] | Biology, NGS, Mapping |
BRATNextGen | 20150505 | [61] | Biology, Genomics |
Bsmap | 2.74, 2.87 | [62] | Biology, NGS, Methylation |
Busco | 1.1b1 | [63] | Biology, Genomics |
Bwa | 0.6.1, 0.7.11, 0.7.12 | [64] | Biology, NGS |
Camino | 20140723 | [65] | Biology, Neuroscience, Imaging |
CAP3 | 20120705 | [66] | Biology, sequence assembly |
CASAVA | 1.8.2 | [67] | Biology, NGS |
CD-HIT | 4.6, 4.6.4 | [68] | Biology, Genomics |
CDO | 1.6.1 | [69] | Climate |
CEAS | 1.0.2 | [70] | Biology, Genomics |
CellProfiler | 2.0 | [71] | Biology, Image Analysis |
CFITSIO | 3.370 | [72] | Library, C |
CGATools | 1.6.0.42 | [73] | Biology, NGS |
Charmm | 36a3 | [74] | Simulation, Chemistry |
Chartdirector | 5.1.0 | [75] | Graphics |
CheckM | 1.0.4 | [76] | Biology, Genomics |
Chimera | 1.7 | [77] | Biology, Modeling |
ChromEvol | 2.0 | [78] | Biology, Phylogenetics |
CIMS | 4.1.2 | [79] | Biology, Genomics |
Circos | 0.63-pre11 | [80] | Biology, Visualization |
CisGenome | 2.0 | [81] | Biology, Genomics, Peak Calling |
Clann | 3.2.3 | [82] | Biology, Phylogenetics |
CLARK | 1.2.2-b | [83] | Biology, Genomics |
CLHEP | 2.2.0.1 | [84] | High Energy Physics |
ClonalFrame | 1.1, 1.2 | [85] | Biology, Genomics, NGS |
ClonalFrameML | 1.25 | [86] | Biology, Genomics, NGS |
ClustalW | 2.1 | [87] | Biology, Genomics |
Cluster3 | 1.52 | [88] | Biology, Genomics |
Clview | 20130402 | [89] | Biology, Genomics |
ClustalO | 1.2.0 | [90] | Biology, Genomics |
CMake | 2.8.8, 2.9.12.1, 3.1.0 | [91] | Programming, Build System |
CMWP | 140518 | [92] | Biology, Genomics |
CNVSeq | 20110715 | [93] | Biology, NGS |
Cobrapy | 0.3.2 | [94] | Biology, Metabolomics, Modeling |
Coevol | 1.3c, 1.4b | [95] | Biology, Phylogenetics |
CoMap | 1.4.1 | [96] | Biology, Genomics |
CONCOCT | 0.3.1 | [97] | Biology, Genomics |
CoNIFER | 0.2.2 | [98] | Biology, Genomics |
Consed | 23.0 | [99] | Biology, Genomics |
Coreutils | 8.23 | [100] | GNU Utilities, Computer Science |
covNMR | 2014 | [101] | Biochemistry |
CPLEX | 12.6.5 | [102] | Optimizer |
CUDA | 4.2, 5.5 | [103] | Programming, Graphics |
Crux | 1.40 | [104] | Biology, Mass-Spectrometry |
Cufflinks | 1.3.0, 2.0.2, 2.2.1 | [105] | Biology, NGS |
Cutadapt | 1.1, 1.7.1, 1.8.1 | [106] | Biology, NGS |
DAKOTA | 5.4.0 | [107] | Computational Science |
DaPars | 0.9.0 | [108] | Biology, NGS, RNA-Seq |
DCMTK | 3.6.0 | [109] | Biology, Neuroscience, Imaging |
DSSAT | 4.5 | [110] | Biology |
DDSCAT | 7.3.0 | [111] | Astrophysics |
DDT | 4.1.0, 4.2.1 | [112] | Software |
DealII | 8.3.0 | [113] | Library |
Delft3D | 3621 | [114] | Hydrodynamics, Physics |
Desmond | 3.0.3.1 | [115] | Simulation, Biology, Chemistry |
DETONATE | 1.9 | [116] | Biology, NGS |
Dalton | 2011 | [117] | Quantum Chemistry |
Diamond | 0.5.1 | [118] | Computational Biology, Genomics |
Dibig Tools | 1.0 | [119] | Bioinformatics, PBS, Torque, Jobs |
DiffReps | 1.55.4 | [120] | Biology, NGS, ChIP-Seq |
Dindel | 1.01 | [121] | Biology, NGS |
DISCOVARdenovo | 52488 | [122] | Biology, NGS |
DIYABC | 1.0.4.43b, 2.0.3 | [123] | Biology, Genomics |
Dlpoly | 4.03.4 | [124] | Simulation, Biology, Chemistry |
Dlpoly-Classic | 1.9 | [125] | Simulation, Biology, Chemistry |
DNA Clust | 3.0 | [126] | Biology, Genomics |
Dock | 6.5, 6.6, 6.7 | [127] | Chemistry, ligand binding prediction |
DOT | 2.0 | [128] | Biology, Bioinformatics, Docking |
Doxygen | 1.8.3.1 | [129] | Programming, Documentation |
DSSP | 2.2.1 | [130] | Biology, Molecular Dynamics |
DTI-TK | 2.3.1 | [131] | Biology, Neurology, Imaging |
EA-Utils | 1.1.2.537 | [132] | Biology, NGS |
ECTools | 20140311, 20141201 | [133] | Biology, Sequencing, Bioinformatics |
EEGLAB | 12.0.2.1b, 13.2.2b, 13.4.4b | [134] | Biology, Matlab |
EIGENSOFT | 4.2, 5.0.1, 6.0.1 | [135] | Biology, Population |
emboss | 6.5.7 | [136] | Biology, multi-tool suite |
EMAN2 | 2.11 | [137] | Biology |
EMIRGE | 20130727 | [138] | Biology, NGS |
Ensembl_Tools | 80 | [139] | Biology, Bioinformatics |
EPACTS | 3.2.6 | [140] | Biology, Bioinformatics, Genomics |
EPOCH | 4.7.3 | [141] | Astronomy, CPPP |
eQTLA | 1.1 | [142] | Biology, Genomics |
Eqtlbma | 1.2.2 | [143] | Biology, Genotyping |
Esmf | 6.3.0rp1 | [144] | Climate |
Espresso | 5.0.1, 5.2.0, 5.2.1 | [145] | Modeling, Physics |
ESPRIT | 201211 | [146] | Biology, NGS, Metagenomics |
ETE2 | 2.1 | [147] | Biology, Phylogenetics |
Eval | 2.2.8 | [148] | Biology, Genomics, GUI |
ExaBayes | 1.2.1, 1.4.1 | [149] | Biology, Phylogenetics |
ExaML | 1.0.5, 1.0.12, 3.0.14 | [150] | Biology, Phylogenetics |
ExomeCNV | 1.4 | [151] | Biology, NGS, Genomics |
Exonerate | 2.2.0 | [152] | Biology, Genomics |
eXpress | 1.3.1 | [153] | Biology, NGS |
FAR | 2.15 | [154] | Biology, Genomics |
FASTA | 34.26.5, 36.3.6d | [155] | Biology, Genomics |
FastML | 3.0 | [156] | Biology, Phylogenetics, ML |
FastQC | 0.9.6, 0.10.1 | [157] | Biology, NGS |
Fastq-tools | 0.7, 0.8 | [158] | Biology, NGS |
FastStructure | 20150112 | [159] | Biology, Genomics |
FastTree | 2.1.7 | [160] | Biology, Phylogenetics |
Fastx_toolkit | 0.0.13.2 | [161] | Biology, NGS |
Fathmm | 20150225 | [162] | Biology, Genomics |
fcGENE | 1.0.7 | [163] | Biology, Genomics, SNP |
Ferret | 6.82 | [164] | Oceanography, Meteorology |
FFmpeg | 2.1.3, 2.8.3 | [165] | Multimedia, audio, video |
FFTW | 3.3.2, 3.3.3 | [166] | Math, Library, C++ |
FLASH | 1.2.10, 1.2.11 | [167] | Biology, Genomics, NGS |
Flexbar | 2.3 | [168] | Biology, Genomics, NGS |
Fluent | 14.5.7, 15.0.7, 16.0 | [169] | Simulation, Fluid Dynamics |
FragGeneScan | 1.16 | [170] | Biology, NGS, Genomics |
FreeBayes | 0.9.15, 0.9.21, 1.0.1 | [171] | Biology, NGS, SNP Calling |
Freesurfer | 5.2.0, 5.3.0 | [172] | Biology, Neurology, Imaging |
FSL | 5.0.2.2 | [173] | Biology, Neurology, Imaging |
Galaxy | latest | [174] | Biology, Chemistry, Other |
GapFiller | 1.11 | [175] | Biology, NGS |
Garli | 2.0, 2.01 | [176] | Biology, Phylogenetics |
GAML | 20150610 | [177] | Biology, NGS |
GARM | 0.7.4 | [178] | Biology, NGS |
GASVPro | 201310 | [179] | Biology, NGS, Genomics |
GATE | 7.0 | [180] | Data Analysis |
GATK | 1.6.9, 3.4.46, 3.5.0 | [181] | Biology, NGS |
Gaussian | G03, G09-A.02, G09-C.01 | [182] | Modeling, Computational Chemistry |
Gblocks | 0.91b | [183] | Genomics, Alignment tool |
GCTA | 1.24.7 | [184] | Biology, Genomics, SNP |
GDAL | 1.11.2 | [185] | Geospatial Data Modeling, Geospatial Library |
Geant4 | 4.10 | [186] | Physics |
GEM | 20130406 | [187] | Biology, NGS |
GEMINI | 4.6.6a, 0.13.1 | [188] | Biology, Genomics, Genetics |
GenBank Tools | 20140130 | [189] | BIology< Genomics |
GeneMark | 2012.04 | [190] | Biology, Genomics, Metagenomics |
GeneSeqer | 20140226 | [191] | Biology, Genomics |
Genewise | 2.2.0 | [192] | Biology, Genomics, Annotation |
Genome STRiP | 2.00.1602 | [193] | Biology, genomics, NGS |
GenomicTools | 2.7.0 | [194] | Biology, NGS |
GenomeTools | 1.5.7 | [195] | Biology, Bioinformatics |
GenSel | 4.90 | [196] | Biology, Genetics |
GET_HOMOLOGUES | 20150529 | [197] | Biology, Genomics |
GKNO | 1.30.18 | [198] | Biology, NGS, |
Git | 1.8.2.1, 1.9.0 | [199] | Development, Revision Control |
Globus | 2.1.3 | [200] | Data Transfer |
GLPK | 4.55 | [201] | Biology, Genomics |
Gmap | 20150612, 20150723 | [202] | Biology, Genomics |
GNU | 4.4.6, 4.7.2 | [203] | Compilers, Programming |
GnuPlot | 4.6.0 | [204] | Graphics, Plotting, Programming |
Grace | 5.1.22 | [205] | Graphics, plotting, 2D |
GrADS | 2.0.1 | [206] | Earth Science |
GramCluster | 1.3 | [207] | Biology, Sequencing |
GraphViz | 2.38.0 | [208] | Graphics, plotting, visualization |
Gromacs | 4.5.5, 4.6.5 | [209] | Chemistry, Modeling, Simulation |
GSNP | 1.0 | [210] | Biology, Bioinformatics, NGS |
GSL | 1.15 | [211] | Library, Math, C++, C |
Gsutil | 4.15 | [212] | Cloud, Storage, Google |
Gubbins | 20150519 | [213] | Biology, Phylogenetics, Genomics |
GULP | 4.0 | [214] | Material Science |
HaMStR | 13.2.2, 13.2.3, 13.2.4 | [215] | Biology, Genomics |
HapCompass | 0.7.7 | [216] | Biology, NGS, Genomics |
Hapsembler | 2.21 | [217] | Biology, Genomics, NGS |
HapTree | 1.0 | [218] | Biology, Genomics, NGS |
HDF4 | 4.2.11 | [219] | Library, Data |
HDF5 | 1.8.9, 1.8.12, 1.8.15 | [220] | Library, Data |
HISAT2 | 2.0.0b, 2.0.1b | [221] | Biology, Sequence Alignment, NGS |
HMMER3 | 3.0, 3.1b1, 3.1b2 | [222] | Biology, Genomics |
HMMSplicer | 0.9.5 | [223] | Biology, Genomics |
HOMER | 4.2 | [224] | Biology, Genomics |
HTMLDoc | 1.2.82 | [225] | Documentation, PDF, HTML |
HTSeq | 0.5.3p3, 0.6.1p1 | [226] | Biology, NGS |
Hyb | 20141126 | [227] | Biology, NGS, RNA-Seq |
HyPhy | 2.1.2.28 | [228] | Biology, Phylogenetics |
Hypre | 1.10.0b, 2.8.0b | [229] | Library, Math, Physics |
IBDNe | 20150815 | [230] | Biology, NGS |
IDBA-UD | 1.0.9, 1.1.0, 1.1.1 | [231] | Biology, NGS |
IDBA-MT | 1.0 | [232] | Biology, NGS |
IEP | 3.6 | [233] | Programming, Python, Editor |
IGB | 8.4.1 | [234] | Biology, Genomics, NGS |
iGTP | 1.1 | [235] | Biology, Bioinformatics, Phylogenetics |
illumiprocessor | 20150803 | [236] | Biology, Sequencing |
IM and IMa | 20091217 | [237] | Biology, Population |
IMa2 | 20120827 | [238] | Biology, Population |
ImageJ | 1.48 | [239] | Image manipulation |
ImageMagick | 6.8.8-9 | [240] | Image manipulation |
Intel Compilers | 11.1, 2012 | [241] | Programming, Compilers |
IOAPI | 3.1 | [242] | Meteorology |
Iprscan | 4.8 | [243] | Biology, Genomics |
IQ-TREE | 1.3.9, 1.3.10, 1.3.11 | [244] | Biology, Phylogenetics |
ITK | 4.3.1 | [245] | Biology, Genomics |
ITK-SNAP | 3.0.0 | [246] | Biology, Neuroscience, Imaging |
JAGS | 3.3.0 | [247] | Statistics |
Java | 1.6.0_31, 1.7.0_02, 1.8.0_31 | [248] | Java Development Kit |
Jellyfish | 2.1.1 | [249] | Biology, NGS |
JModelTest | 2.1.1 | [250] | Biology, Phylogenetics, Genomics |
Julia | 0.3.11 | [251] | Programming, Languages |
KaKs | 1.2 | [252] | Biology, Phylogenetics |
Kent | 20120524 | [253] | Biology, NGS |
Khmer | 1.1, 2.0 | [254] | Biology, NGS |
KING | 1.4 | [255] | Biology, Genomics |
Kallisto | 0.42.3, 0.42.4 | [256] | Biology, NGS, RNA-Seq |
Kmer | 1934 | [257] | Biology, NGS |
KmerGenie | 1.6741 | [258] | Biology, NGS, Utilities |
Kraken | 0.10.4b | [259] | Biology, Genomics, Phylogenetics |
LAMMPS | 28Oct12, 30Sep13, 28Jun14,15May15 | [260] | Molecular Dynamics Simulation |
LAMP | 2.5 | [261] | Biology, Genomics |
Last | 193, 247 | [262] | Biology, Sequence alignment |
Lastz | 1.03.02, 1.02.00 | [263] | Biology, NGS |
LDhat | 2.2a | [264] | Biology, Genomics |
LIBSVM | 3.12 | [265] | Machine Learning |
LIGR | 2.05 | [266] | Biology, Assembly |
LSC | 0.3, 0.3.1 | [267] | Biology, NGS, Error correction |
Loci | 3.3 | [268] | Fluid Dynamics |
LS-DYNA | 700, 711, 800 | [269] | Physics |
Lumpy | 0.2.1 | [270] | Biology, SNP |
LZO | 2.09 | [271] | Library, Data Compression |
MACH | 1.0.18 | [272] | Biology, Genomics |
Mach2VCF | 20150515 | [273] | Biology |
M5tools | 20121126 | [274] | Biology, Bioinformatics, Genomics |
MACS | 1.4.2 | [275] | Biology, ChIP-Seq |
mafft | 6.903, 7.215, 7.245 | [276] | Biology, Multiple sequence alignment |
Maker | 2.25b, 2.31.6, 2.31.8 | [277] | Biology, Annotation, Genomics |
MapSplice | 2.1.7 | [278] | Biology, NGS, RNA-Seq |
MAPminer | 1.1 | [279] | Biology, Phylogenetics |
MassMine | 0.9.5, 0.10.0 | [280] | Data Mining |
Maq | 0.7.1 | [281] | Biology, NGS |
MARK | 2.0.1 | [282] | Statistics |
MarkerMiner | 20150429, 20150511 | [283] | Biology, Genomics |
MaSuRCA | 2.3.2 | [284] | Biology, NGS |
Matlab | 2012a, 2013a, 2014a | [285] | Math, Simulation, Programming |
MATS | 2.1.0, 3.0.8, 3.0.9 | [286] | BIology, NGS |
Mauve | 2.3.1 | [287] | Biology, NGS |
MaxBin | 2.1.1 | [288] | Biology, NGS |
MCarts | 1.0.2 | [289] | Biology, Genomics, Markov models |
MCNP | 5, 6b2 | [290] | Physics |
MCNPX | 2.7.0, 2.7.0-i8 | [291] | Physics |
MEGAN | 5.10.3 | [292] | Biology, NGS |
Megraft | 1.0.2 | [293] | Biology, Sequencing |
Melting | 4.3.1 | [294] | Biology, Genome, RNA, Folding |
Meme | 4.8.1 | [295] | Biology, Motifs, Sequence analysis |
Meraculous | 2.0.5 | [296] | Biology, NGS |
Mercurial | 2.7 | [297] | Development, Revision Control |
Merlin | 1.1.2 | [298] | Biogolgy, SNP |
Metabin | 1.0 | [299] | Biology, Metagenomics |
MetaCluster | 5.0b | [300] | Biology, Metagenomics |
MetaCV | 2.3.0 | [301] | Biology, NGS |
METAL | 20110325 | [302] | Biology, Genomics |
MetAMOS | 1.5.0rc4-20140827 | [303] | Biology, Bioinformatics, Genomics, Assembly |
Metassembler | 1.5 | [304] | Biology, Genomics |
MetaVelvet | 1.2.01 | [305] | Biology, NGS |
Metaxa2 | 2.0.2, 2.1.1 | [306] | Biology, NGS |
MetaGeneMark | 2012.04 | [307] | Biology, Genomics |
Mfold | 3.6 | [308] | Biology, Genomics |
MHAP | 1.6 | [309] | Biology, Sequencing |
MIA | 20130301 | [310] | Biology, NGS |
Midnight Commander | 4.6.1 | [311] | Tools, Utilities |
Migrate-n | 3.3.0, 3.6.6 | [312] | Biology, Population |
Minimac | 1-20130717, 2-20140915, 3-20150727 | [313] | Biology, Genomics |
mira | 3.9.18, 4.0.rc1, 4.0.2 | [314] | Biology, NGS |
MISO | 0.4.9, 0.5.2, 0.5.3 | [315] | Biology, NGS |
MMSEQ | 1.0.8 | [316] | Biology, NGS |
MSMBuilder | 2.5.1 | [317] | Molecular Dynamics |
MOABS | 1.2.9, 1.3.2, 1.3.4 | [318] | Biology, NGS, Genomics |
Modeller | 9.11, 9.13, 9.14 | [319] | Biology, Modeling |
Molden | 5.0 | [320] | Molecular, electronic structure |
MolPro | 2012.1p22 | [321] | Quantum Chemistry, Ab Initio |
mosaik | 2.1.33, 2.2.3 | [322] | Biology,NGS |
Mothur | 1.31.2, 1.36.1 | [323] | Biology, Microbial Ecology |
MOTU | 1.1 | [324] | Biology, Bioinformatics, Genomics |
MP-EST | 1.4 | [325] | Biology, Phylogenetics |
mpiP | 3.4.1 | [326] | Parallel Computing |
MrBayes | 3.2.1, 3.2.4, 3.2.5 | [327] | Biology, Phylogenetics |
MRIcron | 201306 | [328] | Biology, MRI, Imaging |
MUMmer | 3.23 | [329] | Biology, Genomics |
MUSCLE | 3.8.31 | [330] | Biology, Genomics |
MuTect | 1.1.4, 1.1.7 | [331] | Biology, Genomics |
MutSig | 1.4 | [332] | Biology, Genomics |
MZMine | 2.14.2, 2.15, 2.17 | [333] | Biology, Spectroscopy |
NAMD | 2.9 | [334] | Simulation, Chemistry, Biology |
Nanocorrect | 20150727 | [335] | Biology, NGS |
Nanopolish | 20150904 | [336] | Biology |
Nbody | 6 | [337] | Astronomy |
NCBI C++ Toolkit | 12.0.0 | [338] | Biology, C++, Development |
NCL | 6.1.2, 6.3.0 | [339] | Atmosphere Science |
NCO | 4.2.1, 4.4.3 | [340] | Data exchange tools |
Ncview | 2.1.2 | [341] | Data visualization |
NetCDF | 3.4.2, 4.2, 4.3 | [342] | Data exchange, Tools |
Newbler | 2.7, 2.8, 2.9 | [343] | Biology, NGS |
Newick utils | 1.6 | [344] | Biology, Phylogenetics |
Nextallele | 20140718 | [345] | Biology, Genomics |
Nexus NCL | 2.1.18 | [346] | Biology, Phylogenetics, Library |
ngsCAT | 0.1 | [347] | Biology, Bioinformatics, NGS |
ngsTools | 20150816 | [348] | Biology, NGS |
NGSUtils | 20130722, 20150206 | [349] | Biology, NGS |
Nipype | 0.10.0 | [350] | Biology, Bioinformatics, Neuroscience, Imaging |
NMRPipe | 7.9 | [351] | Biology, Biochemistry |
Novoalign | 2.08.02, 3.00.02 | [352] | Biology, NGS |
NWChem | 6.5 | [353] | Chemistry |
Oases | 0.2.08 | [354] | Biology, NGS |
Olego | 1.1.2, 1.1.5, 1.1.6 | [355] | Biology, NGS, RNA-Seq |
OCaml | 4.02.3 | [356] | Programming Languages, Scripting, Development |
Octave | 3.6.4 | [357] | Numerical Computation |
Oncotator | 1.5.2.0, 1.5.3.0, 1.8.0.0 | [358] | Biology, Genomics |
OpenBabel | 2.3.2 | [359] | Biology, Chemistry |
OpenCL | 1.1 | [360] | Programming, Library |
OpenCV | 2.4.8 | [361] | Computervision |
OpenFOAM | 2.1.1 | [362] | Fluid Dynamics |
OpenMM | 6.2.0 | [363] | Quantum Chemistry |
OrthoFinder | 0.2.5 | [364] | Biology, Genomics |
OrthoMCL | 2.0.2, 2.0.3, 2.0.7 | [365] | Biology, Genomics |
p4vasp | 0.3.29 | [366] | Molecular, Electronic Structure |
Pacbio | 2.2.0, 2.3.0 | [367] | Biology, Bioinformatics, NGS |
Package-GFE | 20150701 | [368] | Biology, Genomics |
PALES | 122 | [369] | Physics |
PAML | 4.7, 4.8a, 4.9a | [370] | Biology, Phylogenetics |
Pandaseq | 20140808, 20150627 | [371] | Biology, Bioinformatics, NGS, Sequencing |
PAPI | 5.1.0.2 | [372] | Software, Computing |
Parallel | 20150122 | [373] | Programming, Languages |
ParaView | 4.1.0, 4.2.0, 4.3.0 | [374] | Data Analysis |
PartitionFinder | 1.0.1, 1.1.1 | [375] | Biology, Phylogenetics, Evolution |
Parflow | v615 | [376] | Ecology, Modeling |
PASA | 1.5, 2.0-r20150209 | [377] | Biology, Genomics |
PAUP | 4.0b10 | [378] | Biology, Phylogenetics |
PAUDA | 1.0.1 | [379] | Biology, Bioinformatics, Sequence alignment |
PBCore | 20151201 | [380] | Biology, Bioinformatics |
PBCommand | 20151203 | [381] | Biology, Library |
PBJelly | 14.7.14, 15.2.20 | [382] | Biology, Bioinformatics |
pbsdrmaa | 1.0.17 | [383] | Libraries, Torque |
p4est | 1.1 | [384] | Library |
pbsmrtpipe | 20151202 | [385] | Biology |
PeakSplitter | 1.0 | [386] | Biology, Chip-Seq |
PEAR | 0.9.2, 0.9.6 | [387] | Biology, NGS |
PDT | 3.18 | [388] | Programming, Profiler |
Perl | 5.16.0 | [389] | Programming, Language |
PerM | 0.4.0 | [390] | Biology, NGS |
PETSc | 2.3, 3.3 | [391] | Math, Numerical solvers |
PGDSpider | 2.0.9.0 | [392] | Biology, NGS |
Phenix | 1.8.1069, 1.10.2155 | [393] | Crystallography |
PHYLDOG | 20130418 | [394] | Biology, Genomics, Phylogenetics |
Phyluce | 20140427, 20151103 | [395] | Biology, Phylogenetics |
PfamScan | 1.3 | [396] | Biology, Genomics |
PHITS | 2.52 | [397] | Physics |
PIPE-CLIP | 1.1.0 | [398] | Biology, NGS |
Phonopy | 1.9.2 | [399] | Chemistry |
PHYLIP | 3.696 | [400] | Biology, Phylogenetics |
PhyloBayes | 3.3f, 1.4f MPI | [401] | Biology, Phylogenetics |
Phylosift | 1.1 | [402] | Biology, Genomics, Phylogenetics, Taxonomy |
PhyML | 3.0, 20121109 | [403] | Biology, Phylogenetics |
Picard | 1.72, 1.80, 2.0.1 | [404] | Biology, NGS |
PICRUSt | 1.0.0 | [405] | Biology, Phylogenetics |
Piranha | 1.2.1 | [406] | Biology, Phylogenetics |
PLAST | 1.0 | [407] | Biology, Bioinformatics |
Plink | 1.07, 1.90b3 | [408] | Biology, GWAS |
PLINKSEQ | 0.10 | [409] | Biology, Genomics |
PluMiST | 1.1 | [410] | Biology, Phylogenetics, Genomics |
PolyPhen | 2.2.2.r405b | [411] | Biology, Genomics |
Poretools | 0.5.0 | [412] | Biology, Sequencing |
POV-Ray | 3.7 | [413] | 3D, Graphics |
Preseq | 0.0.4 | [414] | Biology, NGS |
Primer3 | 2.3.4 | [415] | Biology, Genomics |
ProfessAtQE | 2014 | [416] | Material Science, Molecular Dynamics |
Prokka | 1.10, 1.11 | [417] | Biology, Genomics, Bioinformatics, Assembly |
ProBABEL | 0.4.2, 0.4.3, 0.4.5 | [418] | Biology, Genomics, GWAS |
Probalign | 1.4 | [419] | Biology, Genomics |
Proovread | 1.03rcl | [420] | Biology, Genomics, NGS |
Proteinortho | 4.26 | [421] | Biology, Genomics |
PROVEAN | 1.1.5 | [422] | Biology, Genomics |
Python | 2.7.6, 3.5.0 | [423] | Biology, Genomics, NGS |
Pyrad | 3.0.63 | [424] | Biology, Sequencing Alignment, Assembly |
QDD | 3.1.2 | [425] | Programming, scripting, language |
QIIME | 1.5.0 | [426] | Biology, Ecology |
QT | 4.8.3 | [427] | Computer Science |
QUAST | 2.3 | [428] | Biology, NGS |
Quantas | 1.0.4, 1.0.8 | [429] | Biology, Bioinformatics, NGS |
QualiMap | 2.1.1 | [430] | Biology, Sequence alignment |
Quickquartet | 1.0.0 | [431] | Biology, Phylogenetics |
R | Rmpi/2.15.1, 3.0.2, 3.2.0 | [432] | Statistics, Programming |
R8S | 1.71, 1.8 | [433] | Biology, Evolution |
RADICAL | 0.2 | [434] | Biology, Phylogenetics, Genomics |
RAxML | 8.1.23, 8.2.2, 8.2.3 | [435] | Biology, Phylogenetics |
Ray | 2.3.1 | [436] | Biology, Genomics, NGS |
REAPR | 1.0.18 | [437] | Biology, Bioinformatics, Assembly |
RepeatExplorer | 20150506 | [438] | Biology, Genomics |
RepeatMasker | 3.3.0 | [439] | Biology, Genomics |
RepeatModeler | 1.0.8 | [440] | Biology, Bioinformatics |
Reptile | 1.1 | [441] | Biology, NGS, error correction |
riboPicker | 0.4.3 | [442] | Biology, Sequence |
RNAhybrid | 2.1.1 | [443] | Biology, Genomics |
ROOT | 6.0 | [444] | Data Analysis |
Roary | 3.4.1 | [445] | Biology, Genomics |
Rosetta | 2014wk4 | [446] | Biology, Structure, Modelling |
RSEG | 0.4.8 | [447] | Biology, NGS |
RSEM | 1.1.17, 1.2.7, 1.2.19 | [448] | Biology, NGS, RNA-Seq |
RSeQC | 2.3.7, 2.6.2 | [449] | Biology, NGS, RNA-Seq |
Ruby | 1.9.3-p0 | [450] | Programming, Scripting, Language |
Sailfish | 0.6.3 | [451] | Biology, NGS, RNA-Seq |
Sambamba | 0.5.0-dev, 0.5.1 | [452] | Biology, NGS |
Samstat | 1.08 | [453] | Biology, NGS, Bioinformatics, Sequencing |
Samblaster | 0.1.14 | [454] | Biology, NGS |
samtools | 1.0, 1.1, 1.2 | [455] | Biology, NGS |
SAS | 9.3 | [456] | Statistics, Graphing |
SATe | 2.2.7 | [457] | Biology, Phylogenetics |
Scala | 2.11.5 | [458] | Programming, Language |
Scalablast | 2.4.53 | [459] | Biology, Genomics |
Scalpel | 0.1.1 | [460] | Biology, NGS |
SHAPEIT | 2.5.5 | [461] | Biology, SNP |
Sharcgs | 1.2.11 | [462] | Biology, NGS, Assembly |
Schrodinger | 2012, 2013 | [463] | Simulation, chemistry |
SCons | 2.3.0 | [464] | Programming |
SCRATCH1D | 1.0 | [465] | Biology, Genomics |
Scythe | 0.991 | [466] | Biology, NGS |
Segemehl | 0.1.9 | [467] | Biology, NGS, Mapper |
SEPP | 1.0, 3.0 | [468] | Biology, Phylogenetics, HMM |
Seq-Gen | 1.3.3 | [469] | Biology, Phylogenetics |
SeqPrep | 0.5 | [470] | Biology, NGS |
SeqMap | 1.0.13 | [471] | Biology, NGS |
Seqtk | 20140729 | [472] | Biology, NGS |
SEQuel | 1.0.1 | [473] | Biology, NGS |
SeqyClean | 1.8.10 | [474] | Biology, NGS, Bioinformatics |
ShoRAH | 20131204 | [475] | Biology, NGS, quality filter |
SHRiMP | 2.2.3 | [476] | Biology, NGS |
Sickle | 1.200, 1.33 | [477] | Biology, NGS, quality filter |
Siesta | 2.0.2,3.1 | [478] | Simulation, Physics, Ab Initio |
SIFT | 4.0.3b | [479] | Biology, Genomics |
Silo | 4.7 | [480] | Library, Data |
SIPeS | 2.0 | [481] | Biology, Bioinformatics, ChIP-Seq |
Slicer | 4.3.1 | [482] | Biology, Imaging |
SMALT | 0.7.6 | [483] | Biology, NGS |
Snap | 20100728 | [484] | Biology, Genomics |
SNAPE-pooled | 20130407 | [485] | Biology, SNP |
SNeP | 1.1 | [486] | Biology, Phylogenics |
SnpEff | 4.0e, 4.1i, 4.2 | [487] | Biology, NGS, Genomics |
SNPhylo | 20140701 | [488] | Bilogy, Phylogenetics |
SOAPdenovo | 1.05 | [489] | Biology, NGS |
SOAPdenovo-Trans | 1.01, 1.03 | [490] | Biology, NGS |
SOAPsplice | 1.10 | [491] | Biology, NGS |
SparCC | 201402 | [492] | Microbial Ecology |
Spades | 3.5.0, 3.6.0, 3.6.2 | [493] | Biology, NGS |
Spanki | 0.4.1, 0.4.3, 0.5.0 | [494] | Biology, NGS, RNA-Seq |
SPARTA+ | 2.60 | [495] | Chemistry |
Spidey | 20150922 | [496] | Biology, Genomics |
SPIMAP | 1.1 | [497] | Biology, Phylogenetics |
SpliceTrap | 0.90.5 | [498] | Biology, NGS, RNA-Seq |
SPM | 8 | [499] | Biology, Statistics, Neurology, Imaging |
Sputnik | 1.0 | [500] | Biology, Genomics |
SQLite | 3.8.8.2 | [501] | Database |
SQL_Developer | 4.1.2 | [502] | Programming, Oracle, Sql |
SRA | 2.1.10 | [503] | biology, NGS |
SSPACE | 2.0, 3.0 | [504] | Biology, NGS |
Stacks | 1.21, 1.24, 1.35 | [505] | Biology, Genomics, NGS |
STAR | 2.3.0e | [506] | Biology, NGS, Alignment |
STAR-CCM+ | 8.06 | [507] | Mechanical Engineering |
Stata | 10.1, 13 | [508] | Statistics, Data analysis |
Stringtie | 0.97, 1.0.0, 1.1.2 | [509] | Biology, NGS, Alignment |
Structure | 2.3.3, 2.3.4 | [510] | Biology, Population |
SUNDIALS | 2.3.0, 2.5.0 | [511] | Numerical Solver |
SVDetect | 0.8b | [512] | Biology, NGS, SNP |
swak4Foam | 2.x | [513] | Fluid Dynamics |
swarm | 1.2.11 | [514] | Data Analysis |
Swig | 2.0.9 | [515] | Programming, C, C++, Python |
SwitchSeq | 20140907 | [516] | Biology, NGS |
Syzygy | 1.2.7 | [517] | Biology, Genomics |
TASSEL | 5.0 | [518] | Biology, Genomics |
TAU | 2.21.4, 2.23 | [519] | Profiling, Tracing, Programming |
T-Coffee | 9.03.r1318 | [520] | Biology, Genomics, Multiple Alignment |
TESS | 2.3.1 | [521] | Biology, Genomics, Markov |
tgicl | 2.1 | [522] | Biology, sequencing, clustering |
Tmux | 2.0 | [523] | GNU, Terminal Multiplexer |
TomoPy | 0.0.3 | [524] | Biology, Neuroimaging |
Tophat | 1.4.1, 2.0.13, 2.1.0 | [525] | Biology, NGS |
Torch | 20151107 | [526] | Lua |
Totalview | 8.12.0 | [527] | Computer Science |
TPP | 4.7.0 | [528] | Bioinformatics, MassSpec |
TrackTools | 2011 | [529] | Bioinformatics |
TrackVis | 0.5.2.2 | [530] | Biology, Spectroscopy |
Tracula | 5.3.2014_05_26 | [531] | Biology, Bioinformatics, Neuroscience, Imaging |
TraitRate | 1.1 | [532] | Biology, Evolution |
TransDecoder | 20140704, 2.0.1 | [533] | Biology, NGS |
Transrate | 1.0.1 | [534] | Biology, Assembly |
TreeFix | 1.1.7, 1.1.10 | [535] | Biology, Phylogenetics |
TreePL | 20150305 | [536] | Biology, Phylogenetics |
TriMetAss | 1.1 | [537] | Biology, Bioinformatics, NGS |
TRF | 4.04 | [538] | Biology, Genomics |
Trilinos | 11.4.1, 11.8.1 | [539] | Math Algorithm |
trimAl | 1.2 | [540] | Biology, Genomics, Sequence Alignment |
Trim Galore | 0.2.8, 0.4.1 | [541] | Biology, NGS |
Trimmomatic | 0.22, 0.32, 0.33 | [542] | Biology, NGS |
Trinity | r20150302-2.0.6, r20151015-2.1.1 | [543] | Biology, NGS, RNA-Seq |
Trinotate | 2.0.1 | [544] | Biology |
TRNAscan-SE | 1.23 | [545] | Biology, NGS, Bioinformatics |
Twinscan | 4.1.2 | [546] | Biology, Genomics |
usearch | 7.0.1001-64, 8.0.1517 | [547] | Biology, Sequence analysis |
UDUNITS | 2.2.17 | [548] | Library, Units, Programming |
UNAFold | 3.8 | [549] | Biology, Genome, RNA, Folding |
UProC | 1.2.0 | [550] | Biology, Genomics |
Valgrind | 3.9.0 | [551] | Computer Science |
VarScan | 2.3.6 | [552] | Biology, NGS, Genomics |
VASP | 5.3.2, 5.3.3, 5.3.5 | [553] | Quantum Chemistry, Ab Initio |
VAST-TOOLS | 20150506 | [554] | Biology, NGS, RNA-Seq |
VCFLib | 20141119, 20150313 | [555] | Biology, NGS, Genomics |
VCFtools | 0.1.12a, 0.1.12b, 0.1.14 | [556] | Biology, SNPs |
velvet | 1.2.06, 1.2.07, 1.2.10 | [557] | Biology, Genomics, NGS |
VEP | 74 | [558] | Biology, NGS |
VICUNA | 1.3 | [559] | Biology, Assembly |
Vim | 7.4.5 | [560] | Programming, Scripting, Language |
vmd | 1.9.1 | [561] | Biology, Visualization |
VSearch | 20151022 | [562] | Biology, NGS |
VTK | 6.1.0 | [563] | Visualization, Graphics |
Wannier90 | 1.2, 2.0.0 | [564] | Computational Physics |
WebLogo | 3.3 | [565] | Biology, Genomics |
WDSSII | 1 | [566] | Meteorology |
WIEN2k | 12.1 | [567] | Material Science, Chemistry |
Wgs or Celera | 8.2, 8.3rc1, 8.3rc1.r4638 | [568] | Biology, NGS |
wublast | 2.0 | [569] | Biology, Sequence Alignment |
YAHA | 0.1.82 | [570] | Biology NGS |
XCrySDen | 1.5.60 | [571] | Computational Material Science |
Yambo | 3.3.0 | [572] | Physics |
YASM | 1.3.0 | [573] | Computer Science |
Yasra | 2.32 | [574] | Biology, NGS |
Zagros | 1.0.0 | [575] | 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.
Add New App
To add a documentation page for a new piece of software installed into /apps please go to Add New App Page.