Difference between revisions of "Installed Software"

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| <span id="B"></span> [[BamBam]] || 1.0 || [http://udall-lab.byu.edu/Research/Software/BamBam.aspx] || Biology, NGS
 
| <span id="B"></span> [[BamBam]] || 1.0 || [http://udall-lab.byu.edu/Research/Software/BamBam.aspx] || Biology, NGS
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|-
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| [[Bam-readcount]] || 20150216 || [https://github.com/genome/bam-readcount] || Biology, NGS
 
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| [[Bamstats]] || 20140602 || [https://github.com/lindenb/jvarkit/wiki/BamStats04] || Biology, NGS
 
| [[Bamstats]] || 20140602 || [https://github.com/lindenb/jvarkit/wiki/BamStats04] || Biology, NGS

Revision as of 16:29, 25 March 2015

  • Last updated on 2015-03-25.
  • 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
Atlas 3.10.1, 3.11.17 [9] Library, Math
Amuse 6.0 [10] Astrophysics
Affymetrix Power Tools 1.15.0 [11] Biology, Genomics, Microarray
ARC 20140312 [12] Biology, NGS
Astral 4.4.4, 4.7.6 [13] Biology, Bioinformatics, NGS, Phylogenetics
AtomEye 3 [14] Material Science
ATRAM 20140624 [15] Biology, NGS
Augustus 2.6 [16] Biology, NGS
BamBam 1.0 [17] Biology, NGS
Bam-readcount 20150216 [18] Biology, NGS
Bamstats 20140602 [19] Biology, NGS
Bamtools 2.1.1 [20] Biology, NGS
BamUtil 1.0.2 [21] Biology, NGS
BayesRate 1.3.43 [22] Biology, Phylogenetics
Bbcp 12.08.17.00.0 [23] Network file transfer
Bcftools 20140618 [24] Biology, Genomics, NGS
BEAGLE 3.2.2, 4.0 [25] Biology, Genetics, Genotyping
BEAST 1.7.5, 1.8.1, 2.1.3 [26] Biology, Phylogenetics
Bedops 2.4.2 [27] Biology, Bioinformatics, Sequence, NGS
BEDTools 2.16.2, 2.17.0, 2.23.0 [28] Biology, NGS
BEST 2.3 [29] Biology, Phylogenetics
BETA 1.0.5 [30] Biology, NGS
BFAST 0.7.0 [31] Biology, NGS
Bismark 0.7.4, 0.7.7, 0.13.0 [32] Biology, NGS, Methylation
Bioconductor Latest [33] Biology, R, Statistics
BioPerl 1.006901 [34] Biology, Perl
PHYLDOG 20130418 [35] Biology, Genomics, Phylogenetics
Phyluce c561dd9 [36] Biology, Phylogenetics
BioPython 1.59 [37] Biology, Python
BLASR 20130815 [38] Biology, NGS
NCBI BLAST 2.2.27, 2.2.28, 2.2.29 [39] Biology, Sequence alignment
Blast2go 2.5.0-20120705 [40] Biology, Annotation
BLAT 20120524 [41] Biology, Sequence alignment
Blender 2.63 [42] Graphics
Boost 1.49.0, 1.53.0, 1.54.0 [43] C++, Library
Bowtie 0.12.9, 1.0.0, 1.1.1 [44] Biology, NGS
Bowtie2 2.2.2, 2.2.3, 2.2.4, 2.2.5 [45] Biology, NGS
BPP 2.2, 1.9.0 [46] Biology, Phylogenetics
BRANCH 1.8.1 [47] Biology, NGS, Mapping
Bsmap 2.74, 2.87 [48] Biology, NGS, Methylation
Bwa 0.6.1, 0.7.11, 0.7.12 [49] Biology, NGS
Camino 20140723 [50] Biology, Neuroscience, Imaging
CAP3 20120705 [51] Biology, sequence assembly
CASAVA 1.8.2 [52] Biology, NGS
CD-HIT 4.6 [53] Biology, Genomics
CDO 1.6.1 [54] Climate
CEAS 1.0.2 [55] Biology, Genomics
CellProfiler 2.0 [56] Biology, Image Analysis
CGATools 1.6.0.42 [57] Biology, NGS
Charmm 36a3 [58] Simulation, Chemistry
Chartdirector 5.1.0 [59] Graphics
Chimera 1.7 [60] Biology, Modeling
ChromEvol 2.0 [61] Biology, Phylogenetics
CIMS 4.1.2 [62] Biology, Genomics
Circos 0.63-pre11 [63] Biology, Visualization
CisGenome 2.0 [64] Biology, Genomics, Peak Calling
Clann 3.2.3 [65] Biology, Phylogenetics
CLHEP 2.2.0.1 [66] High Energy Physics
ClonalFrame 1.1, 1.2 [67] Biology, Genomics, NGS
ClustalW 2.1 [68] Biology, Genomics
Cluster3 1.52 [69]] Biology, Genomics
Clview 20130402 [70] Biology, Genomics
CMake 2.8.8, 2.9.12.1, 3.1.0 [71] Programming, Build System
CNVSeq 20110715 [72] Biology, NGS
Coevol 1.3c, 1.4b [73] Biology, Phylogenetics
CoMap 1.4.1 [74] Biology, Genomics
CONCOCT 0.3.1 [75] Biology, Genomics
CoNIFER 0.2.2 [76] Biology, Genomics
Consed 23.0 [77] Biology, Genomics
Coreutils 8.23 [78] GNU Utilities, Computer Science
covNMR 2014 [79] Biochemistry
CUDA 4.2, 5.5 [80] Programming, Graphics
Crux 1.40 [81] Biology, Mass-Spectrometry
Cufflinks 1.3.0, 2.0.2, 2.2.1 [82] Biology, NGS
Cutadapt 1.1, 1.7.1 [83] Biology, NGS
DAKOTA 5.4.0 [84] Computational Science
DaPars 0.9.0 [85] Biology, NGS, RNA-Seq
DCMTK 3.6.0 [86] Biology, Neuroscience, Imaging
DSSAT 4.5 [87] Biology
DDSCAT 7.3.0 [88] Astrophysics
DDT 4.1.0, 4.2.1 [89] Software
Delft3D 3621 [90] Hydrodynamics, Physics
Desmond 3.0.3.1 [91] Simulation, Biology, Chemistry
Dalton 2011 [92] Quantum Chemistry
Diamond 0.5.1 [93] Computational Biology, Genomics
Dibig Tools 1.0 [94] Bioinformatics, PBS, Torque, Jobs
DiffReps 1.55.4 [95] Biology, NGS, ChIP-Seq
Dindel 1.01 [96] Biology, NGS
DIYABC 1.0.4.43b, 2.0.3 [97] Biology, Genomics
Dlpoly 4.03.4 [98] Simulation, Biology, Chemistry
DNA Clust 3.0 [99] Biology, Genomics
Dock 6.5, 6.6 [100] Chemistry, ligand binding prediction
DOT 2.0 [101] Biology, Bioinformatics, Docking
Doxygen 1.8.3.1 [102] Programming, Documentation
DSSP 2.2.1 [103] Biology, Molecular Dynamics
DTI-TK 2.3.1 [104] Biology, Neurology, Imaging
EA-Utils 1.1.2.537 [105] Biology, NGS
ECTools 20140311, 20141201 [106] Biology, Sequencing, Bioinformatics
EEGLAB 12.0.2.1b, 13.2.2b, 13.4.4b [107] Biology, Matlab
EIGENSOFT 4.2, 5.0.1 [108] Biology, Population
emboss 6.5.7 [109] Biology, multi-tool suite
EMIRGE 20130727 [110] Biology, NGS
eQTLA 1.1 [111] Biology, Genomics
Eqtlbma 1.2.2 [112] Biology, Genotyping
Espresso 5.0.1 [113] Modeling, Physics
ESPRIT 201211 [114] Biology, NGS, Metagenomics
ETE2 2.1 [115] Biology, Phylogenetics
Eval 2.2.8 [116] Biology, Genomics, GUI
ExaBayes 1.2.1 [117] Biology, Phylogenetics
ExaML 1.0.3, 1.0.5, 1.0.12 [118] Biology, Phylogenetics
ExomeCNV 1.4 [119] Biology, NGS, Genomics
Exonerate 2.2.0 [120] Biology, Genomics
eXpress 1.3.1 [121] Biology, NGS
FAR 2.15 [122] Biology, Genomics
FASTA 34.26.5, 36.3.6d [123] Biology, Genomics
FastML 3.0 [124] Biology, Phylogenetics, ML
FastQC 0.9.6, 0.10.1 [125] Biology, NGS
FastTree 2.1.7 [126] Biology, Phylogenetics
Fastx_toolkit 0.0.13.2 [127] Biology, NGS
fcGENE 1.0.7 [128] Biology, Genomics, SNP
Ferret 6.82 [129] Oceanography, Meteorology
FFmpeg 2.1.3 [130] Multimedia, audio, video
FFTW 3.3.2, 3.3.3 [131] Math, Library, C++
FLASH 1.2.10, 1.2.11 [132] Biology, Genomics, NGS
Flexbar 2.3 [133] Biology, Genomics, NGS
Fluent 14.5.7, 15.0 [134] Simulation, Fluid Dynamics
FragGeneScan 1.16 [135] Biology, NGS, Genomics
FreeBayes 0.9.6, 0.9.15 [136] Biology, NGS, SNP Calling
Freesurfer 5.2.0 [137] Biology, Neurology, Imaging
FSL 5.0.2.2 [138] Biology, Neurology, Imaging
GapFiller 1.11 [139] Biology, NGS
Garli 2.0, 2.01 [140] Biology, Phylogenetics
GASVPro 201310 [141] Biology, NGS, Genomics
GATE 7.0 [142] Data Analysis
GATK 1.6.9, 2.7.4, 3.1.1, 3.3.0 [143] Biology, NGS
Gaussian E01, G03, G09-A.02, G09-C.01 [144] Modeling, Computational Chemistry
Gblocks 0.91b [145] Genomics, Alignment tool
Geant4 4.10 [146] Physics
GEM 20130406 [147] Biology, NGS
GEMINI 4.6.6a [148] Biology, Genomics, Genetics
GenBank Tools 20140130 [149] BIology< Genomics
GeneMark 2012.04 [150] Biology, Genomics, Metagenomics
GeneSeqer 20140226 [151] Biology, Genomics
Genewise 2.2.0 [152] Biology, Genomics, Annotation
GenomicTools 2.7.0 [153] Biology, NGS
GenSel 4.90 [154] Biology, Genetics
GKNO 1.30.18 [155] Biology, NGS
Git 1.8.2.1 [156] Development, Revision Control
Globus 2.1.3 [157] Data Transfer
GLPK 4.55 [158] Biology, Genomics
Gmap 20141222 [159] Biology, Genomics
GNU 4.4.6, 4.7.2 [160] Compilers, Programming
GnuPlot 4.6.0 [161] Graphics, Plotting, Programming
Grace 5.1.22 [162] Graphics, plotting, 2D
GrADS 2.0.1 [163] Earth Science
GraphViz 2.38.0 [164] Graphics, plotting, visualization
Gromacs 4.5.5, 4.6.5 [165] Chemistry, Modeling, Simulation
GSNP 1.0 [166] Biology, Bioinformatics, NGS
GSL 1.15 [167] Library, Math, C++, C
GULP 4.0 [168] Material Science
HaMStR v8b [169] Biology, Genomics
HapCompass 0.7.7 [170] Biology, NGS, Genomics
Hapsembler 2.21 [171] Biology, Genomics, NGS
HapTree 1.0 [172] Biology, Genomics, NGS
HDF4 4.2.11 [173] Library, Data
HDF5 1.8.9, 1.8.12 [174] Library, Data
HMMER3 3.0, 3.1b1 [175] Biology, Genomics
HMMSplicer 0.9.5 [176] Biology, Genomics
HOMER 4.2 [177] Biology, Genomics
HTMLDoc 1.2.82 [178] Documentation, PDF, HTML
HTSeq 0.5.3p3, 0.6.1p1 [179] Biology, NGS
HyPhy 2.1.2.28 [180] Biology, Phylogenetics
Hypre 1.10.0b, 2.8.0b [181] Library, Math, Physics
IDBA-UD 1.0.9, 1.1.0 [182] Biology, NGS
iGTP 1.1 [183] Biology, Bioinformatics, Phylogenetics
IM and IMa 20091217 [184] Biology, Population
IMa2 20120827 [185] Biology, Population
ImageJ 1.48 [186] Image manipulation
ImageMagick 6.8.8-9 [187] Image manipulation
Intel Compilers 11.1, 2012 [188] Programming, Compilers
IOAPI 3.1 [189] Meteorology
Iprscan 4.8 [190] Biology, Genomics
ITK 4.3.1 [191] Biology, Genomics
ITK-SNAP 3.0.0 [192] Biology, Neuroscience, Imaging
JAGS 3.3.0 [193] Statistics
Java 1.6.0_31, 1.7.0_02, 1.8.0_31 [194] Java Development Kit
Jellyfish 2.1.1 [195] Biology, NGS
JModelTest 2.1.1. [196] Biology, Phylogenetics, Genomics
KaKs 1.2 [197] Biology, Phylogenetics
Kent 20120524 [198] Biology, NGS
Khmer 1.1 [199] Biology, NGS
KING 1.4 [200] Biology, Genomics
Kmer 1934 [201] Biology, NGS
KmerGenie 1.6741 [202] Biology, NGS, Utilities
Kraken 0.10.4b [203] Biology, Genomics, Phylogenetics
LAMMPS 28Oct12, 30Sep13, 28Jun14 [204] Molecular Dynamics Simulation
Last 193, 247 [205] Biology, Sequence alignment
Lastz 1.03.02, 1.02.00 [206] Biology, NGS
LIBSVM 3.12 [207] Machine Learning
LSC 0.3, 0.3.1 [208] Biology, NGS, Error correction
Loci 3.3 [209] Fluid Dynamics
LS-DYNA 700, 711 [210] Physics
Lumpy 0.2.1 [211] Biology, SNP
LZO 2.09 [212] Library, Data Compression
MACH 1.0.18 [213] Biology, Genomics
M5tools 20121126 [214] Biology, Bioinformatics, Genomics
MACS 1.4.2 [215] Biology, ChIP-Seq
mafft 7.037, 6.903, 7.215 [216] Biology, Multiple sequence alignment
Maker 2.10, 2.25b [217] Biology, Annotation, Genomics
MapSplice 2.1.7 [218] Biology, NGS, RNA-Seq
Maq 0.7.1 [219] Biology, NGS
MARK 2.0.1 [220] Statistics
MaSuRCA 2.3.2 [221] Biology, NGS
Matlab 2012a, 2013a, 2014a [222] Math, Simulation, Programming
MATS 2.1.0, 3.0.6b, 3.0.8, 3.0.9 [223] BIology, NGS
Mauve 2.3.1 [224] Biology, NGS
MCarts 1.0.2 [225] Biology, Genomics, Markov models
MCNP 5, 6b2 [226] Physics
MCNPX 2.7.0, 2.7.0-i8 [227] Physics
Melting 4.3.1 [228] Biology, Genome, RNA, Folding
Meme 4.8.1 [229] Biology, Motifs, Sequence analysis
Mercurial 2.7 [230] Development, Revision Control
Metabin 1.0 [231] Biology, Metagenomics
MetaCluster 5.0beta [232] Biology, Metagenomics
MetaCV 2.3.0 [233] Biology, NGS
METAL 20110325 [234] Biology, Genomics
MetAMOS 1.5.0rc4-20140827 [235] Biology, Bioinformatics, Genomics, Assembly
MetaVelvet 1.2.01 [236] Biology, NGS
MetaGeneMark 2012.04 [237] Biology, Genomics
Mfold 3.6 [238] Biology, Genomics
MIA 20130301 [239] Biology, NGS
Midnight Commander 4.6.1 [240] Tools, Utilities
Migrate-n 3.3.0 [241] Biology, Population
mira 3.9.9, 3.9.18, 4.0.rc1 [242] Biology, NGS
MISO 0.4.4, 0.4.9 [243] Biology, NGS
MMSEQ 1.0.8 [244] Biology, NGS
MSMBuilder 2.5.1 [245] Molecular Dynamics
MOABS 1.2.9 [246] Biology, NGS, Genomics
Modeller 9.11, 9.13, 9.14 [247] Biology, Modeling
Molden 5.0 [248] Molecular, electronic structure
MolPro 2012.1p22 [249] Quantum Chemistry, Ab Initio
mosaik 2.1.33 [250] Biology,NGS
Mothur 1.31.2 [251] Biology, Microbial Ecology
MOTU 1.1 [252] Biology, Bioinformatics, Genomics
MP-EST 1.4 [253] Biology, Phylogenetics
mpiP 3.4.1 [254] Parallel Computing
MrBayes 3.2.1 [255] Biology, Phylogenetics
MRIcron 201306 [256] Biology, MRI, Imaging
MUMmer 3.23 [257] Biology, Genomics
MUSCLE 3.8.31 [258] Biology, Genomics
MZMine 2.10 [259] Biology, Spectroscopy
NAMD 2.9 [260] Simulation, Chemistry, Biology
Nbody 6 [261] Astronomy
NCBI C++ Toolkit 12.0.0 [262] Biology, C++, Development
NCL 6.1.2 [263] Atmosphere Science
NCO 4.2.1, 4.4.3 [264] Data exchange tools
Ncview 2.1.2 [265] Data visualization
NetCDF 3.4.2, 4.2, 4.3 [266] Data exchange, Tools
Newbler 2.6, 2.7 [267] Biology, NGS
Newick utils 1.6 [268] Biology, Phylogenetics
Nextallele 20140718 [269] Biology, Genomics
Nexus NCL 2.1.18 [270] Biology, Phylogenetics, Library
ngsCAT 0.1 [271] Biology, Bioinformatics, NGS
NGSUtils 20130722, 20150206 [272] Biology, NGS
Nipype 0.10.0 [273] Biology, Bioinformatics, Neuroscience, Imaging
NMRPipe 7.9 [274] Biology, Biochemistry
Novoalign 2.08.02, 3.00.02 [275] Biology, NGS
Oases 0.2.08 [276] Biology, NGS
Olego 1.1.2, 1.1.5 [277] Biology, NGS, RNA-Seq
Octave 3.6.4 [278] Numerical Computation
OpenBabel 2.3.2 [279] Biology, Chemistry
OpenCL 1.1 [280] Programming, Library
OpenCV 2.4.8 [281] Computervision
OpenFOAM 2.1.1 [282] Fluid Dynamics
OpenMM 6.2.0 [283] Quantum Chemistry
OrthoMCL 2.0.2, 2.0.3, 2.0.7 [284] Biology, Genomics
p4vasp 0.3.29 [285] Molecular, Electronic Structure
Pacbio 2.2.0.133377 [286] Biology, Bioinformatics, NGS
PALES 122 [287] Physics
PAML 4.7, 4.8a [288] Biology, Phylogenetics
Pandaseq 20140808 [289] Biology, Bioinformatics, NGS, Sequencing
PAPI 5.1.0.2 [290] Software, Computing
Parallel 20150122 [291] Programming, Languages
ParaView 4.1.0 [292] Data Analysis
PartitionFinder 1.0.1, 1.1.1 [293] Biology, Phylogenetics, Evolution
Parflow v615 [294] Ecology, Modeling
PASA 1.5, 2.0-r20150209 [295] Biology, Genomics
PAUP 4.0b10 [296] Biology, Phylogenetics
PBJelly 14.7.14 [297] Biology, Bioinformatics
pbsdrmaa 1.0.17 [298] Libraries, Torque
PeakSplitter 1.0 [299] Biology, Chip-Seq
PEAR 0.9.2, 0.9.6 [300] Biology, NGS
PDT 3.18 [301] Programming, Profiler
Perl 5.16.0 [302] Programming, Language
PerM 0.4.0 [303] Biology, NGS
PETSc 2.3, 3.3 [304] Math, Numerical solvers
Phenix 1.8.1069 [305] Crystallography
PfamScan 1.3 [306] Biology, Genomics
PHITS 2.52 [307] Physics
Phonopy 1.9.2 [308] Chemistry
PhyloBayes 3.3f, 1.4f MPI [309] Biology, Phylogenetics
Phylosift 1.1 [310] Biology, Genomics, Phylogenetics, Taxonomy
PhyML 3.0, 20121109 [311] Biology, Phylogenetics
Picard 1.69, 1.72, 1.80 [312] Biology, NGS
PLAST 1.0 [313] Biology, Bioinformatics
Plink 1.07 [314] Biology, GWAS
PLINKSEQ 0.10 [315] Biology, Genomics
PluMiST 1.1 [316] Biology, Phylogenetics, Genomics
Preseq 0.0.4 [317] Biology, NGS
Primer3 2.3.4 [318] Biology, Genomics
Prokka 1.10 [319] Biology, Genomics, Bioinformatics, Assembly
ProBABEL 0.4.2, 0.4.3 [320] Biology, Genomics, GWAS
Probalign 1.4 [321] Biology, Genomics
Proovread 1.03rcl [322] Biology, Genomics, NGS
Proteinortho 4.26 [323] Biology, Genomics
python 2.6.8, 2.7.3, 2.7.5, 2.7.6, 2.7.8 [324] Biology, Genomics, NGS
QDD 3.1.2 [325] Programming, scripting, language
QIIME 1.5.0 [326] Biology, Ecology
QT 4.8.3 [327] Computer Science
QUAST 2.3 [328] Biology, NGS
Quickquartet 1.0.0 [329] Biology, Phylogenetics
R Rmpi/2.15.1, 33.0.2 [330] Statistics, Programming
R8S 1.71 [331] Biology, Evolution
RADICAL 0.2 [332] Biology, Phylogenetics, Genomics
RAxML 7.9.1, 8.0.25, 8.1.12 [333] Biology, Phylogenetics
RepeatMasker 3.3.0 [334] Biology, Genomics
Reptile 1.1 [335] Biology, NGS, error correction
riboPicker 0.4.3 [336] Biology, Sequence
RNAhybrid 2.1.1 [337] Biology, Genomics
ROOT 6.0 [338] Data Analysis
Rosetta 2014wk4 [339] Biology, Structure, Modelling
RSEG 0.4.8 [340] Biology, NGS
RSEM 1.1.17, 1.2.7, 1.2.19 [341] Biology, NGS, RNA-Seq
Ruby 1.9.3-p0 [342] Programming, Scripting, Language
Sailfish 0.6.3 [343] Biology, NGS, RNA-Seq
Sambamba 0.5.0-dev, 0.5.1 [344] Biology, NGS
Samstat 1.08 [345] Biology, NGS, Bioinformatics, Sequencing
Samblaster 0.1.14 [346] Biology, NGS
samtools 1.0, 1.1, 1.2 [347] Biology, NGS
SAS 9.3 [348] Statistics, Graphing
SATe 2.2.7 [349] Biology, Phylogenetics
Scalablast 2.4.53, 2.11.5 [350] Biology, Genomics
Scalpel 0.1.1 [351] Biology, NGS
Sharcgs 1.2.11 [352] Biology, NGS, Assembly
Schrodinger 2012, 2013 [353] Simulation, chemistry
SCons 2.3.0 [354] Programming
SCRATCH1D 1.0 [355] Biology, Genomics
Scythe 0.991 [356] Biology, NGS
Segemehl 0.1.9 [357] Biology, NGS, Mapper
SeqPrep 0.5 [358] Biology, NGS
SeqMap 1.0.13 [359] Biology, NGS
Seqtk 20140729 [360] Biology, NGS
SEQuel 1.0.1 [361] Biology, NGS
SeqyClean 1.8.10 [362] Biology, NGS, Bioinformatics
ShoRAH 20131204 [363] Biology, NGS, quality filter
SHRiMP 2.2.3 [364] Biology, NGS
Sickle 1.200, 1.33 [365] Biology, NGS, quality filter
Siesta 2.0.2,3.1 [366] Simulation, Physics, Ab Initio
SIFT 4.0.3b [367] Biology, Genomics
Silo 4.7 [368] Library, Data
SIPeS 2.0 [369] Biology, Bioinformatics, ChIP-Seq
Slicer 4.3.1 [370] Biology, Imaging
SMALT 0.7.6 [371] Biology, NGS
Snap 20100728 [372] Biology, Genomics
SnpEff 3.3h, 4.0e [373] Biology, NGS, Genomics
SOAPdenovo 1.05 [374] Biology, NGS
SOAPdenovo-Trans 1.01, 1.03 [375] Biology, NGS
SOAPsplice 1.10 [376] Biology, NGS
SparCC 201402 [377] Microbial Ecology
Spades 3.0.0, 3.1.0, 3.5.0 [378] Biology, NGS
Spanki 0.4.1, 0.4.3 [379] Biology, NGS, RNA-Seq
SPARTA+ 2.60 [380] Chemistry
SPIMAP 1.1 [381] Biology, Phylogenetics
SpliceTrap 0.90.5 [382] Biology, NGS, RNA-Seq
SPM 8 [383] Biology, Statistics, Neurology, Imaging
Sputnik 1.0 [384] Biology, Genomics
SQLite 3.8.8.2 [385] Database
SRA 2.1.10 [386]] biology, NGS
SSPACE 2.0 [387] Biology, NGS
Stacks 0.9995 [388] Biology, Genomics, NGS
STAR 2.3.0e [389] Biology, NGS, Alignment
STAR-CCM+ 8.06 [390] Mechanical Engineering
Stata 10.1, 13 [391] Statistics, Data analysis
Stringtie 0.97 [392] Biology, NGS, Alignment
Structure 2.3.3, 2.3.4 [393] Biology, Population
SUNDIALS 2.3.0, 2.5.0 [394] Numerical Solver
SVDetect 0.8b [395] Biology, NGS, SNP
swak4Foam 2.x [396] Fluid Dynamics
swarm 1.2.11 [397] Data Analysis
Swig 2.0.9 [398] Programming, C, C++, Python
SwitchSeq 20140907 [399] Biology, NGS
Syzygy 1.2.7 [400] Biology, Genomics
TASSEL 5.0 [401] Biology, Genomics
TAU 2.21.4, 2.23 [402] Profiling, Tracing, Programming
T-Coffee 9.03.r1318 [403] Biology, Genomics, Multiple Alignment
TESS 2.3.1 [404] Biology, Genomics, Markov
tgicl 2.1 [405] Biology, sequencing, clustering
TomoPy 0.0.3 [406] Biology, Neuroimaging
Tophat 1.4.1, 2.0.13 [407] Biology, NGS
Totalview 8.12.0 [408] Computer Science
TPP 4.7.0 [409] Bioinformatics, MassSpec
TrackTools 2011 [410] Bioinformatics
TrackVis 0.5.2.2 [411] Biology, Spectroscopy
Tracula 5.3.2014_05_26 [412] Biology, Bioinformatics, Neuroscience, Imaging
TraitRate 1.1 [413] Biology, Evolution
TransDecoder 20140704 [414] Biology, NGS
TreeFix 1.1.7 [415] Biology, Phylogenetics
TRF 4.04 [416] Biology, Genomics
Trilinos 11.4.1, 11.8.1 [417] Math Algorithm
Trim Galore 0.2.8 [418] Biology, NGS
Trimmomatic 0.22, 0.32 [419] Biology, NGS
Trinity r20140413, r20150215-2.0.4 [420] Biology, NGS, RNA-Seq
TRNAscan-SE 1.23 [421] Biology, NGS, Bioinformatics
Twinscan 4.1.2 [422] Biology, Genomics
usearch 7.0.1001-64, 8.0.1517 [423] Biology, Sequence analysis
UDUNITS 2.2.17 [424] Library, Units, Programming
UNAFold 3.8 [425] Biology, Genome, RNA, Folding
Valgrind 3.9.0 [426] Computer Science
VASP 5.3.2, 5.3.3, 5.3.5 [427] Quantum Chemistry, Ab Initio
VarScan 2.3.6 [428] Biology, NGS, Genomics
VCFLib 20121207 [429] Biology, NGS, Genomics
VCFtools 0.1.9, 0.1.10 [430] Biology, SNPs
velvet 1.2.06, 1.2.07, 1.2.10 [431] Biology, Genomics, NGS
VEP 74 [432] Biology, NGS
Vim 7.4.5-minimal, 7.4.5-py2, 7.4.5 [433] Programming, Scripting, Language
vmd 1.9.1 [434] Biology, Visualization
VTK 6.1.0 [435] Visualization, Graphics
Wannier90 1.2, 2.0.0 [436] Computational Physics
WebLogo 3.3 [437] Biology, Genomics
WDSSII 1 [438] Meteorology
WIEN2k 12.1 [439] Material Science, Chemistry
Wgs or Celera 8.1, 8.2, 8.3rc1 [440] Biology, NGS
wublast 2.0 [441] Biology, Sequence Alignment
YAHA 0.1.82 [442] Biology NGS
XCrySDen 1.5.60 [443] Computational Material Science
Yambo 3.3.0 [444] Physics
Yasra 2.32 [445] Biology, NGS
  1. ↑ 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.

Retrieved from "https://help.rc.ufl.edu/mediawiki/index.php?title=Installed_Software&oldid=13424"