Difference between revisions of "Installed Software"

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| [[covNMR]] || 2014 || [http://spin.ccic.ohio-state.edu/index.php/welcome/index] || Biochemistry
 
| [[covNMR]] || 2014 || [http://spin.ccic.ohio-state.edu/index.php/welcome/index] || Biochemistry
 +
|-
 +
| [[CPLEX]] || 12.6.5 || [http://www-01.ibm.com/software/commerce/optimization/cplex-optimizer/] || Optimizer
 
|-
 
|-
 
| [[CUDA]] || 4.2, 5.5 || [http://www.nvidia.com/object/cuda_home_new.html] || Programming, Graphics
 
| [[CUDA]] || 4.2, 5.5 || [http://www.nvidia.com/object/cuda_home_new.html] || Programming, Graphics

Revision as of 20:52, 7 May 2015

  • Last updated on 2015-05-07.
  • 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
ANGSD 20150306 [11] Biology, NGS
Affymetrix Power Tools 1.15.0 [12] Biology, Genomics, Microarray
ARC 20140312 [13] Biology, NGS
Astral 4.4.4, 4.7.6 [14] Biology, Bioinformatics, NGS, Phylogenetics
AtomEye 3 [15] Material Science
ATRAM 20140624 [16] Biology, NGS
Augustus 2.6 [17] Biology, NGS
BamBam 1.0 [18] Biology, NGS
Bam-readcount 20150216 [19] Biology, NGS
Bamstats 20140602 [20] Biology, NGS
Bamtools 2.1.1 [21] Biology, NGS
BamUtil 1.0.2 [22] Biology, NGS
BayesRate 1.3.43 [23] Biology, Phylogenetics
Bbcp 12.08.17.00.0 [24] Network file transfer
Bcbio-nextgen 0.8.7 [25] Biology, NGS
Bcftools 1.0, 1.2 [26] Biology, Genomics, NGS
BEAGLE 3.2.2, 4.0 [27] Biology, Genetics, Genotyping
BEAST 1.7.5, 1.8.1, 2.1.3 [28] Biology, Phylogenetics
Bedops 2.4.2 [29] Biology, Bioinformatics, Sequence, NGS
BEDTools 2.16.2, 2.17.0, 2.23.0 [30] Biology, NGS
BEST 2.3 [31] Biology, Phylogenetics
BETA 1.0.5 [32] Biology, NGS
BFAST 0.7.0 [33] Biology, NGS
Bismark 0.7.4, 0.7.7, 0.13.0 [34] Biology, NGS, Methylation
Bioconductor Latest [35] Biology, R, Statistics
BioPerl 1.006901 [36] Biology, Perl
PHYLDOG 20130418 [37] Biology, Genomics, Phylogenetics
Phyluce c561dd9 [38] Biology, Phylogenetics
BioPython 1.59 [39] Biology, Python
BLASR 20130815 [40] Biology, NGS
NCBI BLAST 2.2.27, 2.2.28, 2.2.29 [41] Biology, Sequence alignment
Blast2go 2.5.0-20120705 [42] Biology, Annotation
BLAT 20120524 [43] Biology, Sequence alignment
Blender 2.63 [44] Graphics
Boost 1.49.0, 1.53.0, 1.54.0 [45] C++, Library
Bowtie 0.12.9, 1.0.0, 1.1.1 [46] Biology, NGS
Bowtie2 2.2.2, 2.2.3, 2.2.4, 2.2.5 [47] Biology, NGS
BPP 2.2, 1.9.0 [48] Biology, Phylogenetics
BRANCH 1.8.1 [49] Biology, NGS, Mapping
Bsmap 2.74, 2.87 [50] Biology, NGS, Methylation
Bwa 0.6.1, 0.7.11, 0.7.12 [51] Biology, NGS
Camino 20140723 [52] Biology, Neuroscience, Imaging
CAP3 20120705 [53] Biology, sequence assembly
CASAVA 1.8.2 [54] Biology, NGS
CD-HIT 4.6 [55] Biology, Genomics
CDO 1.6.1 [56] Climate
CEAS 1.0.2 [57] Biology, Genomics
CellProfiler 2.0 [58] Biology, Image Analysis
CGATools 1.6.0.42 [59] Biology, NGS
Charmm 36a3 [60] Simulation, Chemistry
Chartdirector 5.1.0 [61] Graphics
Chimera 1.7 [62] Biology, Modeling
ChromEvol 2.0 [63] Biology, Phylogenetics
CIMS 4.1.2 [64] Biology, Genomics
Circos 0.63-pre11 [65] Biology, Visualization
CisGenome 2.0 [66] Biology, Genomics, Peak Calling
Clann 3.2.3 [67] Biology, Phylogenetics
CLHEP 2.2.0.1 [68] High Energy Physics
ClonalFrame 1.1, 1.2 [69] Biology, Genomics, NGS
ClustalW 2.1 [70] Biology, Genomics
Cluster3 1.52 [71]] Biology, Genomics
Clview 20130402 [72] Biology, Genomics
CMake 2.8.8, 2.9.12.1, 3.1.0 [73] Programming, Build System
CNVSeq 20110715 [74] Biology, NGS
Coevol 1.3c, 1.4b [75] Biology, Phylogenetics
CoMap 1.4.1 [76] Biology, Genomics
CONCOCT 0.3.1 [77] Biology, Genomics
CoNIFER 0.2.2 [78] Biology, Genomics
Consed 23.0 [79] Biology, Genomics
Coreutils 8.23 [80] GNU Utilities, Computer Science
covNMR 2014 [81] Biochemistry
CPLEX 12.6.5 [82] Optimizer
CUDA 4.2, 5.5 [83] Programming, Graphics
Crux 1.40 [84] Biology, Mass-Spectrometry
Cufflinks 1.3.0, 2.0.2, 2.2.1 [85] Biology, NGS
Cutadapt 1.1, 1.7.1 [86] Biology, NGS
DAKOTA 5.4.0 [87] Computational Science
DaPars 0.9.0 [88] Biology, NGS, RNA-Seq
DCMTK 3.6.0 [89] Biology, Neuroscience, Imaging
DSSAT 4.5 [90] Biology
DDSCAT 7.3.0 [91] Astrophysics
DDT 4.1.0, 4.2.1 [92] Software
Delft3D 3621 [93] Hydrodynamics, Physics
Desmond 3.0.3.1 [94] Simulation, Biology, Chemistry
DETONATE 1.9 [95] Biology, NGS
Dalton 2011 [96] Quantum Chemistry
Diamond 0.5.1 [97] Computational Biology, Genomics
Dibig Tools 1.0 [98] Bioinformatics, PBS, Torque, Jobs
DiffReps 1.55.4 [99] Biology, NGS, ChIP-Seq
Dindel 1.01 [100] Biology, NGS
DIYABC 1.0.4.43b, 2.0.3 [101] Biology, Genomics
Dlpoly 4.03.4 [102] Simulation, Biology, Chemistry
DNA Clust 3.0 [103] Biology, Genomics
Dock 6.5, 6.6 [104] Chemistry, ligand binding prediction
DOT 2.0 [105] Biology, Bioinformatics, Docking
Doxygen 1.8.3.1 [106] Programming, Documentation
DSSP 2.2.1 [107] Biology, Molecular Dynamics
DTI-TK 2.3.1 [108] Biology, Neurology, Imaging
EA-Utils 1.1.2.537 [109] Biology, NGS
ECTools 20140311, 20141201 [110] Biology, Sequencing, Bioinformatics
EEGLAB 12.0.2.1b, 13.2.2b, 13.4.4b [111] Biology, Matlab
EIGENSOFT 4.2, 5.0.1 [112] Biology, Population
emboss 6.5.7 [113] Biology, multi-tool suite
EMIRGE 20130727 [114] Biology, NGS
eQTLA 1.1 [115] Biology, Genomics
Eqtlbma 1.2.2 [116] Biology, Genotyping
Espresso 5.0.1 [117] Modeling, Physics
ESPRIT 201211 [118] Biology, NGS, Metagenomics
ETE2 2.1 [119] Biology, Phylogenetics
Eval 2.2.8 [120] Biology, Genomics, GUI
ExaBayes 1.2.1 [121] Biology, Phylogenetics
ExaML 1.0.3, 1.0.5, 1.0.12 [122] Biology, Phylogenetics
ExomeCNV 1.4 [123] Biology, NGS, Genomics
Exonerate 2.2.0 [124] Biology, Genomics
eXpress 1.3.1 [125] Biology, NGS
FAR 2.15 [126] Biology, Genomics
FASTA 34.26.5, 36.3.6d [127] Biology, Genomics
FastML 3.0 [128] Biology, Phylogenetics, ML
FastQC 0.9.6, 0.10.1 [129] Biology, NGS
FastTree 2.1.7 [130] Biology, Phylogenetics
Fastx_toolkit 0.0.13.2 [131] Biology, NGS
fcGENE 1.0.7 [132] Biology, Genomics, SNP
Ferret 6.82 [133] Oceanography, Meteorology
FFmpeg 2.1.3 [134] Multimedia, audio, video
FFTW 3.3.2, 3.3.3 [135] Math, Library, C++
FLASH 1.2.10, 1.2.11 [136] Biology, Genomics, NGS
Flexbar 2.3 [137] Biology, Genomics, NGS
Fluent 14.5.7, 15.0 [138] Simulation, Fluid Dynamics
FragGeneScan 1.16 [139] Biology, NGS, Genomics
FreeBayes 0.9.6, 0.9.15, 0.9.21 [140] Biology, NGS, SNP Calling
Freesurfer 5.2.0 [141] Biology, Neurology, Imaging
FSL 5.0.2.2 [142] Biology, Neurology, Imaging
GapFiller 1.11 [143] Biology, NGS
Garli 2.0, 2.01 [144] Biology, Phylogenetics
GARM 0.7.4 [145] Biology, NGS
GASVPro 201310 [146] Biology, NGS, Genomics
GATE 7.0 [147] Data Analysis
GATK 1.6.9, 2.7.4, 3.1.1, 3.3.0 [148] Biology, NGS
Gaussian G03, G09-A.02, G09-C.01 [149] Modeling, Computational Chemistry
Gblocks 0.91b [150] Genomics, Alignment tool
Geant4 4.10 [151] Physics
GEM 20130406 [152] Biology, NGS
GEMINI 4.6.6a, 0.13.1 [153] Biology, Genomics, Genetics
GenBank Tools 20140130 [154] BIology< Genomics
GeneMark 2012.04 [155] Biology, Genomics, Metagenomics
GeneSeqer 20140226 [156] Biology, Genomics
Genewise 2.2.0 [157] Biology, Genomics, Annotation
GenomicTools 2.7.0 [158] Biology, NGS
GenSel 4.90 [159] Biology, Genetics
GKNO 1.30.18 [160] Biology, NGS
Git 1.8.2.1 [161] Development, Revision Control
Globus 2.1.3 [162] Data Transfer
GLPK 4.55 [163] Biology, Genomics
Gmap 20141222 [164] Biology, Genomics
GNU 4.4.6, 4.7.2 [165] Compilers, Programming
GnuPlot 4.6.0 [166] Graphics, Plotting, Programming
Grace 5.1.22 [167] Graphics, plotting, 2D
GrADS 2.0.1 [168] Earth Science
GraphViz 2.38.0 [169] Graphics, plotting, visualization
Gromacs 4.5.5, 4.6.5 [170] Chemistry, Modeling, Simulation
GSNP 1.0 [171] Biology, Bioinformatics, NGS
GSL 1.15 [172] Library, Math, C++, C
GULP 4.0 [173] Material Science
HaMStR 13.2.2, 13.2.3 [174] Biology, Genomics
HapCompass 0.7.7 [175] Biology, NGS, Genomics
Hapsembler 2.21 [176] Biology, Genomics, NGS
HapTree 1.0 [177] Biology, Genomics, NGS
HDF4 4.2.11 [178] Library, Data
HDF5 1.8.9, 1.8.12 [179] Library, Data
HMMER3 3.0, 3.1b1 [180] Biology, Genomics
HMMSplicer 0.9.5 [181] Biology, Genomics
HOMER 4.2 [182] Biology, Genomics
HTMLDoc 1.2.82 [183] Documentation, PDF, HTML
HTSeq 0.5.3p3, 0.6.1p1 [184] Biology, NGS
HyPhy 2.1.2.28 [185] Biology, Phylogenetics
Hypre 1.10.0b, 2.8.0b [186] Library, Math, Physics
IDBA-UD 1.0.9, 1.1.0 [187] Biology, NGS
IEP 3.6 [188] Programming, Python, Editor
iGTP 1.1 [189] Biology, Bioinformatics, Phylogenetics
IM and IMa 20091217 [190] Biology, Population
IMa2 20120827 [191] Biology, Population
ImageJ 1.48 [192] Image manipulation
ImageMagick 6.8.8-9 [193] Image manipulation
Intel Compilers 11.1, 2012 [194] Programming, Compilers
IOAPI 3.1 [195] Meteorology
Iprscan 4.8 [196] Biology, Genomics
ITK 4.3.1 [197] Biology, Genomics
ITK-SNAP 3.0.0 [198] Biology, Neuroscience, Imaging
JAGS 3.3.0 [199] Statistics
Java 1.6.0_31, 1.7.0_02, 1.8.0_31 [200] Java Development Kit
Jellyfish 2.1.1 [201] Biology, NGS
JModelTest 2.1.1. [202] Biology, Phylogenetics, Genomics
KaKs 1.2 [203] Biology, Phylogenetics
Kent 20120524 [204] Biology, NGS
Khmer 1.1 [205] Biology, NGS
KING 1.4 [206] Biology, Genomics
Kmer 1934 [207] Biology, NGS
KmerGenie 1.6741 [208] Biology, NGS, Utilities
Kraken 0.10.4b [209] Biology, Genomics, Phylogenetics
LAMMPS 28Oct12, 30Sep13, 28Jun14 [210] Molecular Dynamics Simulation
LAMP 2.5 [211] Biology, Genomics
Last 193, 247 [212] Biology, Sequence alignment
Lastz 1.03.02, 1.02.00 [213] Biology, NGS
LIBSVM 3.12 [214] Machine Learning
LSC 0.3, 0.3.1 [215] Biology, NGS, Error correction
Loci 3.3 [216] Fluid Dynamics
LS-DYNA 700, 711 [217] Physics
Lumpy 0.2.1 [218] Biology, SNP
LZO 2.09 [219] Library, Data Compression
MACH 1.0.18 [220] Biology, Genomics
M5tools 20121126 [221] Biology, Bioinformatics, Genomics
MACS 1.4.2 [222] Biology, ChIP-Seq
mafft 7.037, 6.903, 7.215 [223] Biology, Multiple sequence alignment
Maker 2.10, 2.25b [224] Biology, Annotation, Genomics
MapSplice 2.1.7 [225] Biology, NGS, RNA-Seq
Maq 0.7.1 [226] Biology, NGS
MARK 2.0.1 [227] Statistics
MarkerMiner 20150429 [228] Biology, Genomics
MaSuRCA 2.3.2 [229] Biology, NGS
Matlab 2012a, 2013a, 2014a [230] Math, Simulation, Programming
MATS 2.1.0, 3.0.6b, 3.0.8, 3.0.9 [231] BIology, NGS
Mauve 2.3.1 [232] Biology, NGS
MCarts 1.0.2 [233] Biology, Genomics, Markov models
MCNP 5, 6b2 [234] Physics
MCNPX 2.7.0, 2.7.0-i8 [235] Physics
MEGAN 5.10.3 [236] Biology, NGS
Melting 4.3.1 [237] Biology, Genome, RNA, Folding
Meme 4.8.1 [238] Biology, Motifs, Sequence analysis
Mercurial 2.7 [239] Development, Revision Control
Metabin 1.0 [240] Biology, Metagenomics
MetaCluster 5.0beta [241] Biology, Metagenomics
MetaCV 2.3.0 [242] Biology, NGS
METAL 20110325 [243] Biology, Genomics
MetAMOS 1.5.0rc4-20140827 [244] Biology, Bioinformatics, Genomics, Assembly
MetaVelvet 1.2.01 [245] Biology, NGS
MetaGeneMark 2012.04 [246] Biology, Genomics
Mfold 3.6 [247] Biology, Genomics
MIA 20130301 [248] Biology, NGS
Midnight Commander 4.6.1 [249] Tools, Utilities
Migrate-n 3.3.0 [250] Biology, Population
mira 3.9.9, 3.9.18, 4.0.rc1 [251] Biology, NGS
MISO 0.4.4, 0.4.9, 0.5.2, 0.5.3 [252] Biology, NGS
MMSEQ 1.0.8 [253] Biology, NGS
MSMBuilder 2.5.1 [254] Molecular Dynamics
MOABS 1.2.9 [255] Biology, NGS, Genomics
Modeller 9.11, 9.13, 9.14 [256] Biology, Modeling
Molden 5.0 [257] Molecular, electronic structure
MolPro 2012.1p22 [258] Quantum Chemistry, Ab Initio
mosaik 2.1.33 [259] Biology,NGS
Mothur 1.31.2 [260] Biology, Microbial Ecology
MOTU 1.1 [261] Biology, Bioinformatics, Genomics
MP-EST 1.4 [262] Biology, Phylogenetics
mpiP 3.4.1 [263] Parallel Computing
MrBayes 3.2.1, 3.2.4, 3.2.5 [264] Biology, Phylogenetics
MRIcron 201306 [265] Biology, MRI, Imaging
MUMmer 3.23 [266] Biology, Genomics
MUSCLE 3.8.31 [267] Biology, Genomics
MZMine 2.10, 2.14.2 [268] Biology, Spectroscopy
NAMD 2.9 [269] Simulation, Chemistry, Biology
Nbody 6 [270] Astronomy
NCBI C++ Toolkit 12.0.0 [271] Biology, C++, Development
NCL 6.1.2 [272] Atmosphere Science
NCO 4.2.1, 4.4.3 [273] Data exchange tools
Ncview 2.1.2 [274] Data visualization
NetCDF 3.4.2, 4.2, 4.3 [275] Data exchange, Tools
Newbler 2.6, 2.7 [276] Biology, NGS
Newick utils 1.6 [277] Biology, Phylogenetics
Nextallele 20140718 [278] Biology, Genomics
Nexus NCL 2.1.18 [279] Biology, Phylogenetics, Library
ngsCAT 0.1 [280] Biology, Bioinformatics, NGS
NGSUtils 20130722, 20150206 [281] Biology, NGS
Nipype 0.10.0 [282] Biology, Bioinformatics, Neuroscience, Imaging
NMRPipe 7.9 [283] Biology, Biochemistry
Novoalign 2.08.02, 3.00.02 [284] Biology, NGS
NWChem 6.5 [285] Chemistry
Oases 0.2.08 [286] Biology, NGS
Olego 1.1.2, 1.1.5 [287] Biology, NGS, RNA-Seq
Octave 3.6.4 [288] Numerical Computation
OpenBabel 2.3.2 [289] Biology, Chemistry
OpenCL 1.1 [290] Programming, Library
OpenCV 2.4.8 [291] Computervision
OpenFOAM 2.1.1 [292] Fluid Dynamics
OpenMM 6.2.0 [293] Quantum Chemistry
OrthoFinder 0.2.5 [294] Biology, Genomics
OrthoMCL 2.0.2, 2.0.3, 2.0.7 [295] Biology, Genomics
p4vasp 0.3.29 [296] Molecular, Electronic Structure
Pacbio 2.2.0, 2.3.0 [297] Biology, Bioinformatics, NGS
PALES 122 [298] Physics
PAML 4.7, 4.8a [299] Biology, Phylogenetics
Pandaseq 20140808 [300] Biology, Bioinformatics, NGS, Sequencing
PAPI 5.1.0.2 [301] Software, Computing
Parallel 20150122 [302] Programming, Languages
ParaView 4.1.0, 4.2.0, 4.3.0 [303] Data Analysis
PartitionFinder 1.0.1, 1.1.1 [304] Biology, Phylogenetics, Evolution
Parflow v615 [305] Ecology, Modeling
PASA 1.5, 2.0-r20150209 [306] Biology, Genomics
PAUP 4.0b10 [307] Biology, Phylogenetics
PBJelly 14.7.14 [308] Biology, Bioinformatics
pbsdrmaa 1.0.17 [309] Libraries, Torque
PeakSplitter 1.0 [310] Biology, Chip-Seq
PEAR 0.9.2, 0.9.6 [311] Biology, NGS
PDT 3.18 [312] Programming, Profiler
Perl 5.16.0 [313] Programming, Language
PerM 0.4.0 [314] Biology, NGS
PETSc 2.3, 3.3 [315] Math, Numerical solvers
Phenix 1.8.1069 [316] Crystallography
PfamScan 1.3 [317] Biology, Genomics
PHITS 2.52 [318] Physics
Phonopy 1.9.2 [319] Chemistry
PhyloBayes 3.3f, 1.4f MPI [320] Biology, Phylogenetics
Phylosift 1.1 [321] Biology, Genomics, Phylogenetics, Taxonomy
PhyML 3.0, 20121109 [322] Biology, Phylogenetics
Picard 1.69, 1.72, 1.80 [323] Biology, NGS
PLAST 1.0 [324] Biology, Bioinformatics
Plink 1.07 [325] Biology, GWAS
PLINKSEQ 0.10 [326] Biology, Genomics
PluMiST 1.1 [327] Biology, Phylogenetics, Genomics
Preseq 0.0.4 [328] Biology, NGS
Primer3 2.3.4 [329] Biology, Genomics
Prokka 1.10 [330] Biology, Genomics, Bioinformatics, Assembly
ProBABEL 0.4.2, 0.4.3 [331] Biology, Genomics, GWAS
Probalign 1.4 [332] Biology, Genomics
Proovread 1.03rcl [333] Biology, Genomics, NGS
Proteinortho 4.26 [334] Biology, Genomics
python 2.7.3, 2.7.5, 2.7.6, 2.7.8 [335] Biology, Genomics, NGS
QDD 3.1.2 [336] Programming, scripting, language
QIIME 1.5.0 [337] Biology, Ecology
QT 4.8.3 [338] Computer Science
QUAST 2.3 [339] Biology, NGS
Quickquartet 1.0.0 [340] Biology, Phylogenetics
R Rmpi/2.15.1, 3.0.2, 3.2.0 [341] Statistics, Programming
R8S 1.71 [342] Biology, Evolution
RADICAL 0.2 [343] Biology, Phylogenetics, Genomics
RAxML 7.9.1, 8.0.25, 8.1.12 [344] Biology, Phylogenetics
RepeatMasker 3.3.0 [345] Biology, Genomics
Reptile 1.1 [346] Biology, NGS, error correction
riboPicker 0.4.3 [347] Biology, Sequence
RNAhybrid 2.1.1 [348] Biology, Genomics
ROOT 6.0 [349] Data Analysis
Rosetta 2014wk4 [350] Biology, Structure, Modelling
RSEG 0.4.8 [351] Biology, NGS
RSEM 1.1.17, 1.2.7, 1.2.19 [352] Biology, NGS, RNA-Seq
Ruby 1.9.3-p0 [353] Programming, Scripting, Language
Sailfish 0.6.3 [354] Biology, NGS, RNA-Seq
Sambamba 0.5.0-dev, 0.5.1 [355] Biology, NGS
Samstat 1.08 [356] Biology, NGS, Bioinformatics, Sequencing
Samblaster 0.1.14 [357] Biology, NGS
samtools 1.0, 1.1, 1.2 [358] Biology, NGS
SAS 9.3 [359] Statistics, Graphing
SATe 2.2.7 [360] Biology, Phylogenetics
Scalablast 2.4.53, 2.11.5 [361] Biology, Genomics
Scalpel 0.1.1 [362] Biology, NGS
Sharcgs 1.2.11 [363] Biology, NGS, Assembly
Schrodinger 2012, 2013 [364] Simulation, chemistry
SCons 2.3.0 [365] Programming
SCRATCH1D 1.0 [366] Biology, Genomics
Scythe 0.991 [367] Biology, NGS
Segemehl 0.1.9 [368] Biology, NGS, Mapper
SeqPrep 0.5 [369] Biology, NGS
SeqMap 1.0.13 [370] Biology, NGS
Seqtk 20140729 [371] Biology, NGS
SEQuel 1.0.1 [372] Biology, NGS
SeqyClean 1.8.10 [373] Biology, NGS, Bioinformatics
ShoRAH 20131204 [374] Biology, NGS, quality filter
SHRiMP 2.2.3 [375] Biology, NGS
Sickle 1.200, 1.33 [376] Biology, NGS, quality filter
Siesta 2.0.2,3.1 [377] Simulation, Physics, Ab Initio
SIFT 4.0.3b [378] Biology, Genomics
Silo 4.7 [379] Library, Data
SIPeS 2.0 [380] Biology, Bioinformatics, ChIP-Seq
Slicer 4.3.1 [381] Biology, Imaging
SMALT 0.7.6 [382] Biology, NGS
Snap 20100728 [383] Biology, Genomics
SnpEff 3.3h, 4.0e [384] Biology, NGS, Genomics
SOAPdenovo 1.05 [385] Biology, NGS
SOAPdenovo-Trans 1.01, 1.03 [386] Biology, NGS
SOAPsplice 1.10 [387] Biology, NGS
SparCC 201402 [388] Microbial Ecology
Spades 3.0.0, 3.1.0, 3.5.0 [389] Biology, NGS
Spanki 0.4.1, 0.4.3 [390] Biology, NGS, RNA-Seq
SPARTA+ 2.60 [391] Chemistry
SPIMAP 1.1 [392] Biology, Phylogenetics
SpliceTrap 0.90.5 [393] Biology, NGS, RNA-Seq
SPM 8 [394] Biology, Statistics, Neurology, Imaging
Sputnik 1.0 [395] Biology, Genomics
SQLite 3.8.8.2 [396] Database
SRA 2.1.10 [397]] biology, NGS
SSPACE 2.0 [398] Biology, NGS
Stacks 0.9995 [399] Biology, Genomics, NGS
STAR 2.3.0e [400] Biology, NGS, Alignment
STAR-CCM+ 8.06 [401] Mechanical Engineering
Stata 10.1, 13 [402] Statistics, Data analysis
Stringtie 0.97 [403] Biology, NGS, Alignment
Structure 2.3.3, 2.3.4 [404] Biology, Population
SUNDIALS 2.3.0, 2.5.0 [405] Numerical Solver
SVDetect 0.8b [406] Biology, NGS, SNP
swak4Foam 2.x [407] Fluid Dynamics
swarm 1.2.11 [408] Data Analysis
Swig 2.0.9 [409] Programming, C, C++, Python
SwitchSeq 20140907 [410] Biology, NGS
Syzygy 1.2.7 [411] Biology, Genomics
TASSEL 5.0 [412] Biology, Genomics
TAU 2.21.4, 2.23 [413] Profiling, Tracing, Programming
T-Coffee 9.03.r1318 [414] Biology, Genomics, Multiple Alignment
TESS 2.3.1 [415] Biology, Genomics, Markov
tgicl 2.1 [416] Biology, sequencing, clustering
TomoPy 0.0.3 [417] Biology, Neuroimaging
Tophat 1.4.1, 2.0.13 [418] Biology, NGS
Totalview 8.12.0 [419] Computer Science
TPP 4.7.0 [420] Bioinformatics, MassSpec
TrackTools 2011 [421] Bioinformatics
TrackVis 0.5.2.2 [422] Biology, Spectroscopy
Tracula 5.3.2014_05_26 [423] Biology, Bioinformatics, Neuroscience, Imaging
TraitRate 1.1 [424] Biology, Evolution
TransDecoder 20140704 [425] Biology, NGS
TreeFix 1.1.7 [426] Biology, Phylogenetics
TRF 4.04 [427] Biology, Genomics
Trilinos 11.4.1, 11.8.1 [428] Math Algorithm
Trim Galore 0.2.8 [429] Biology, NGS
Trimmomatic 0.22, 0.32 [430] Biology, NGS
Trinity r20140413, r20150215-2.0.4 [431] Biology, NGS, RNA-Seq
TRNAscan-SE 1.23 [432] Biology, NGS, Bioinformatics
Twinscan 4.1.2 [433] Biology, Genomics
usearch 7.0.1001-64, 8.0.1517 [434] Biology, Sequence analysis
UDUNITS 2.2.17 [435] Library, Units, Programming
UNAFold 3.8 [436] Biology, Genome, RNA, Folding
Valgrind 3.9.0 [437] Computer Science
VASP 5.3.2, 5.3.3, 5.3.5 [438] Quantum Chemistry, Ab Initio
VarScan 2.3.6 [439] Biology, NGS, Genomics
VCFLib 20141119, 20150313 [440] Biology, NGS, Genomics
VCFtools 0.1.11, 0.1.12a, 0.1.12b [441] Biology, SNPs
velvet 1.2.06, 1.2.07, 1.2.10 [442] Biology, Genomics, NGS
VEP 74 [443] Biology, NGS
Vim 7.4.5-minimal, 7.4.5-py2, 7.4.5 [444] Programming, Scripting, Language
vmd 1.9.1 [445] Biology, Visualization
VTK 6.1.0 [446] Visualization, Graphics
Wannier90 1.2, 2.0.0 [447] Computational Physics
WebLogo 3.3 [448] Biology, Genomics
WDSSII 1 [449] Meteorology
WIEN2k 12.1 [450] Material Science, Chemistry
Wgs or Celera 8.2, 8.3rc1, wgs/8.3rc1.r4638 [451] Biology, NGS
wublast 2.0 [452] Biology, Sequence Alignment
YAHA 0.1.82 [453] Biology NGS
XCrySDen 1.5.60 [454] Computational Material Science
Yambo 3.3.0 [455] Physics
YASM 1.3.0 [456] Computer Science
Yasra 2.32 [457] 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=13533"