Difference between revisions of "Installed Software"

From UFRC
Jump to navigation Jump to search
Line 602: Line 602:
 
| [[PeakSplitter]] || 1.0 || [http://www.ebi.ac.uk/bertone/software.html]|| Biology, Chip-Seq
 
| [[PeakSplitter]] || 1.0 || [http://www.ebi.ac.uk/bertone/software.html]|| Biology, Chip-Seq
 
|-
 
|-
−
| [[PEAR]] || 0.9.2 || [http://www.exelixis-lab.org/web/software/pear] || Biology, NGS
+
| [[PEAR]] || 0.9.2, 0.9.6 || [http://www.exelixis-lab.org/web/software/pear] || Biology, NGS
 
|-
 
|-
 
| [[PDT]] || 3.18 || [http://www.cs.uoregon.edu/Research/pdt/home.php]|| Programming, Profiler
 
| [[PDT]] || 3.18 || [http://www.cs.uoregon.edu/Research/pdt/home.php]|| Programming, Profiler

Revision as of 01:43, 5 March 2015

Installed Software List

Last updated 2015-03-05.

Note: Click on the icons to the right of the column headings to sort the table.

0-9 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 Z

Name Version [1] Website Category
AbInit 6.12.3, 7.10.2 [1] Ab Initio Quantum Chemistry, Density Functional Theory
Abyss 1.3.4, 1.3.7 [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 20120621,20121023,20130321 [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
Bamstats 20140602 [18] Biology, NGS
Bamtools 2.1.1 [19] Biology, NGS
BamUtil 1.0.2 [20] Biology, NGS
BayesRate 1.3.43 [21] Biology, Phylogenetics
Bbcp 12.08.17.00.0 [22] Network file transfer
Bcftools 20140618 [23] Biology, Genomics, NGS
BEAGLE 3.2.2 [24] Biology, Genetics, Genotyping
BEAST 1.7.5, 1.8.1, 2.1.3 [25] Biology, Phylogenetics
Bedops 2.4.2 [26] Biology, Bioinformatics, Sequence, NGS
BEDTools 2.16.2, 2.17.0, 2.23.0 [27] Biology, NGS
BEST 2.3 [28] Biology, Phylogenetics
BETA 1.0.5 [29] Biology, NGS
BFAST 0.7.0 [30] Biology, NGS
Bismark 0.7.4, 0.7.7, 0.13.0 [31] Biology, NGS, Methylation
Bioconductor Latest [32] Biology, R, Statistics
BioPerl 1.006901 [33] Biology, Perl
PHYLDOG 20130418 [34] Biology, Genomics, Phylogenetics
Phyluce c561dd9 [35] Biology, Phylogenetics
BioPython 1.59 [36] Biology, Python
BLASR 20130815 [37] Biology, NGS
NCBI BLAST 2.2.27, 2.2.28, 2.2.29 [38] Biology, Sequence alignment
Blast2go 2.5.0-20120705 [39] Biology, Annotation
BLAT 20120524 [40] Biology, Sequence alignment
Blender 2.63 [41] Graphics
Boost 1.49.0, 1.53.0, 1.54.0 [42] C++, Library
Bowtie 0.12.9, 1.0.0 [43] Biology, NGS
Bowtie2 2.1.0, 2.2.2, 2.2.3, 2.2.4 [44] Biology, NGS
BPP 2.2, 1.9.0 [45] Biology, Phylogenetics
BRANCH 1.8.1 [46] Biology, NGS, Mapping
Bsmap 2.74, 2.87 [47] Biology, NGS, Methylation
Bwa 0.6.1, 0.7.11, 0.7.12 [48] Biology, NGS
Camino 20140723 [49] Biology, Neuroscience, Imaging
CAP3 20120705 [50] Biology, sequence assembly
CASAVA 1.8.2 [51] Biology, NGS
CD-HIT 4.6 [52] Biology, Genomics
CDO 1.6.1 [53] Climate
CEAS 1.0.2 [54] Biology, Genomics
CellProfiler 2.0 [55] Biology, Image Analysis
CGATools 1.6.0.42 [56] Biology, NGS
Charmm 36a3 [57] Simulation, Chemistry
Chartdirector 5.1.0 [58] Graphics
Chimera 1.7 [59] Biology, Modeling
ChromEvol 2.0 [60] Biology, Phylogenetics
CIMS 4.1.2 [61] Biology, Genomics
Circos 0.63-pre11 [62] Biology, Visualization
CisGenome 2.0 [63] Biology, Genomics, Peak Calling
Clann 3.2.3 [64] Biology, Phylogenetics
CLHEP 2.2.0.1 [65] High Energy Physics
ClonalFrame 1.1, 1.2 [66] Biology, Genomics, NGS
ClustalW 2.1 [67] Biology, Genomics
Cluster3 1.52 [68]] Biology, Genomics
Clview 20130402 [69] Biology, Genomics
CMake 2.8.8, 2.9.12.1, 3.1.0 [70] Programming, Build System
CNVSeq 20110715 [71] Biology, NGS
Coevol 1.3c, 1.4b [72] Biology, Phylogenetics
CoMap 1.4.1 [73] Biology, Genomics
CONCOCT 0.3.1 [74] Biology, Genomics
Consed 23.0 [75] Biology, Genomics
Coreutils 8.23 [76] GNU Utilities, Computer Science
covNMR 2014 [77] Biochemistry
CUDA 4.2, 5.5 [78] Programming, Graphics
Crux 1.40 [79] Biology, Mass-Spectrometry
Cufflinks 1.3.0, 2.0.2, 2.2.1 [80] Biology, NGS
Cutadapt 1.1, 1.7.1 [81] Biology, NGS
DAKOTA 5.4.0 [82] Computational Science
DaPars 0.9.0 [83] Biology, NGS, RNA-Seq
DCMTK 3.6.0 [84] Biology, Neuroscience, Imaging
DSSAT 4.5 [85] Biology
DDSCAT 7.3.0 [86] Astrophysics
DDT 4.1.0, 4.2.1 [87] Software
Delft3D 3621 [88] Hydrodynamics, Physics
Desmond 3.0.3.1 [89] Simulation, Biology, Chemistry
Dalton 2011 [90] Quantum Chemistry
Diamond 0.5.1 [91] Computational Biology, Genomics
Dibig Tools 1.0 [92] Bioinformatics, PBS, Torque, Jobs
DiffReps 1.55.4 [93] Biology, NGS, ChIP-Seq
Dindel 1.01 [94] Biology, NGS
DIYABC 1.0.4.43b, 2.0.3 [95] Biology, Genomics
Dlpoly 4.03.4 [96] Simulation, Biology, Chemistry
DNA Clust 3.0 [97] Biology, Genomics
Dock 6.5, 6.6 [98] Chemistry, ligand binding prediction
DOT 2.0 [99] Biology, Bioinformatics, Docking
Doxygen 1.8.3.1 [100] Programming, Documentation
DSSP 2.2.1 [101] Biology, Molecular Dynamics
DTI-TK 2.3.1 [102] Biology, Neurology, Imaging
E EA-Utils 1.1.2.537 [103] Biology, NGS
ECTools 20140311, 20141201 [104] Biology, Sequencing, Bioinformatics
EEGLAB 12.0.2.1b [105] Biology, Matlab
EIGENSOFT 4.2, 5.0.1 [106] Biology, Population
emboss 6.5.7 [107] Biology, multi-tool suite
EMIRGE 20130727 [108] Biology, NGS
eQTLA 1.1 [109] Biology, Genomics
Eqtlbma 1.2.2 [110] Biology, Genotyping
Espresso 5.0.1 [111] Modeling, Physics
ESPRIT 201211 [112] Biology, NGS, Metagenomics
ETE2 2.1 [113] Biology, Phylogenetics
Eval 2.2.8 [114] Biology, Genomics, GUI
ExaBayes 1.2.1 [115] Biology, Phylogenetics
ExaML 1.0.3, 1.0.5, 1.0.12 [116] Biology, Phylogenetics
ExomeCNV 1.4 [117] Biology, NGS, Genomics
Exonerate 2.2.0 [118] Biology, Genomics
eXpress 1.3.1 [119] Biology, NGS
FAR 2.15 [120] Biology, Genomics
FASTA 34.26.5, 36.3.6d [121] Biology, Genomics
FastML 3.0 [122] Biology, Phylogenetics, ML
FastQC 0.9.6, 0.10.1 [123] Biology, NGS
FastTree 2.1.7 [124] Biology, Phylogenetics
Fastx_toolkit 0.0.13.2 [125] Biology, NGS
fcGENE 1.0.7 [126] Biology, Genomics, SNP
Ferret 6.82 [127] Oceanography, Meteorology
FFmpeg 2.1.3 [128] Multimedia, audio, video
FFTW 3.3.2, 3.3.3 [129] Math, Library, C++
FLASH 1.2.10, 1.2.11 [130] Biology, Genomics, NGS
Flexbar 2.3 [131] Biology, Genomics, NGS
Fluent 14.5.7, 15.0 [132] Simulation, Fluid Dynamics
FragGeneScan 1.16 [133] Biology, NGS, Genomics
FreeBayes 0.9.6, 0.9.15 [134] Biology, NGS, SNP Calling
Freesurfer 5.2.0 [135] Biology, Neurology, Imaging
FSL 5.0.2.2 [136] Biology, Neurology, Imaging
G GapFiller 1.11 [137] Biology, NGS
Garli 2.0, 2.01 [138] Biology, Phylogenetics
GASVPro 201310 [139] Biology, NGS, Genomics
GATE 7.0 [140] Data Analysis
GATK 1.6.9, 2.7.4, 3.1.1, 3.3.0 [141] Biology, NGS
Gaussian E01, G03, G09-A.02, G09-C.01 [142] Modeling, Computational Chemistry
Gblocks 0.91b [143] Genomics, Alignment tool
Geant4 4.10 [144] Physics
GEM 20130406 [145] Biology, NGS
GEMINI 4.6.6a [146] Biology, Genomics, Genetics
GenBank Tools 20140130 [147] BIology< Genomics
GeneMark 2012.04 [148] Biology, Genomics, Metagenomics
Genewise 2.2.0 [149] Biology, Genomics, Annotation
GenomicTools 2.7.0 [150] Biology, NGS
GenSel 4.90 [151] Biology, Genetics
GKNO 1.30.18 [152] Biology, NGS
Git 1.8.2.1 [153] Development, Revision Control
Globus 2.1.3 [154] Data Transfer
GLPK 4.55 [155] Biology, Genomics
Gmap 20130618, 20130720, 20140530 [156] Biology, Genomics
GNU 4.4.6, 4.7.2 [157] Compilers, Programming
GnuPlot 4.6.0 [158] Graphics, Plotting, Programming
Grace 5.1.22 [159] Graphics, plotting, 2D
GrADS 2.0.1 [160] Earth Science
GraphViz 2.38.0 [161] Graphics, plotting, visualization
Gromacs 4.5.5, 4.6.5 [162] Chemistry, Modeling, Simulation
GSNP 1.0 [163] Biology, Bioinformatics, NGS
GSL 1.15 [164] Library, Math, C++, C
GULP 4.0 [165] Material Science
HaMStR v8b [166] Biology, Genomics
HapCompass 0.7.7 [167] Biology, NGS, Genomics
Hapsembler 2.21 [168] Biology, Genomics, NGS
HapTree 1.0 [169] Biology, Genomics, NGS
HDF4 4.2.11 [170] Library, Data
HDF5 1.8.9, 1.8.12 [171] Library, Data
HMMER3 3.0, 3.1b1 [172] Biology, Genomics
HMMSplicer 0.9.5 [173] Biology, Genomics
HOMER 4.2 [174] Biology, Genomics
HTMLDoc 1.2.82 [175] Documentation, PDF, HTML
HTSeq 0.5.3p3, 0.6.1p1 [176] Biology, NGS
HyPhy 2.1.2.28 [177] Biology, Phylogenetics
Hypre 1.10.0b, 2.8.0b [178] Library, Math, Physics
IDBA-UD 1.0.9, 1.1.0 [179] Biology, NGS
iGTP 1.1 [180] Biology, Bioinformatics, Phylogenetics
IM and IMa 20091217 [181] Biology, Population
IMa2 20120827 [182] Biology, Population
ImageJ 1.48 [183] Image manipulation
ImageMagick 6.8.8-9 [184] Image manipulation
Intel Compilers 11.1, 2012 [185] Programming, Compilers
IOAPI 3.1 [186] Meteorology
Iprscan 4.8 [187] Biology, Genomics
ITK 4.3.1 [188] Biology, Genomics
ITK-SNAP 3.0.0 [189] Biology, Neuroscience, Imaging
JAGS 3.3.0 [190] Statistics
Java 1.6.0_31, 1.7.0_02, 1.8.0_31 [191] Java Development Kit
Jellyfish 2.1.1 [192] Biology, NGS
JModelTest 2.1.1. [193] Biology, Phylogenetics, Genomics
KaKs 1.2 [194] Biology, Phylogenetics
Kent 20120524 [195] Biology, NGS
Khmer 1.1 [196] Biology, NGS
KING 1.4 [197] Biology, Genomics
Kmer 1934 [198] Biology, NGS
KmerGenie 1.6741 [199] Biology, NGS, Utilities
Kraken 0.10.4b [200] Biology, Genomics, Phylogenetics
LAMMPS 28Oct12, 30Sep13, 28Jun14 [201] Molecular Dynamics Simulation
Last 193, 247 [202] Biology, Sequence alignment
Lastz 1.03.02, 1.02.00 [203] Biology, NGS
LIBSVM 3.12 [204] Machine Learning
LSC 0.3, 0.3.1 [205] Biology, NGS, Error correction
Loci 3.3 [206] Fluid Dynamics
LS-DYNA 700, 711 [207] Physics
Lumpy 0.2.1 [208] Biology, SNP
MACH 1.0.18 [209] Biology, Genomics
M5tools 20121126 [210] Biology, Bioinformatics, Genomics
MACS 1.4.2 [211] Biology, ChIP-Seq
mafft 7.037, 6.903, 7.215 [212] Biology, Multiple sequence alignment
Maker 2.10, 2.25b [213] Biology, Annotation, Genomics
MapSplice 2.1.7 [214] Biology, NGS, RNA-Seq
Maq 0.7.1 [215] Biology, NGS
MARK 2.0.1 [216] Statistics
MaSuRCA 2.3.2 [217] Biology, NGS
Matlab 2012a, 2013a, 2014a [218] Math, Simulation, Programming
MATS 2.1.0, 3.0.6b, 3.0.8, 3.0.9 [219] BIology, NGS
Mauve 2.3.1 [220] Biology, NGS
MCarts 1.0.2 [221] Biology, Genomics, Markov models
MCNP 5, 6b2 [222] Physics
MCNPX 2.7.0, 2.7.0-i8 [223] Physics
Melting 4.3.1 [224] Biology, Genome, RNA, Folding
Meme 4.8.1 [225] Biology, Motifs, Sequence analysis
Mercurial 2.7 [226] Development, Revision Control
Metabin 1.0 [227] Biology, Metagenomics
MetaCluster 5.0beta [228] Biology, Metagenomics
MetaCV 2.3.0 [229] Biology, NGS
METAL 20110325 [230] Biology, Genomics
MetAMOS 1.5.0rc4-20140827 [231] Biology, Bioinformatics, Genomics, Assembly
MetaVelvet 1.2.01 [232] Biology, NGS
MetaGeneMark 2012.04 [233] Biology, Genomics
Mfold 3.6 [234] Biology, Genomics
MIA 20130301 [235] Biology, NGS
Midnight Commander 4.6.1 [236] Tools, Utilities
Migrate-n 3.3.0 [237] Biology, Population
mira 3.2.0, 3.4.0.1, 3.9.9, 3.9.18, 4.0.rc1 [238] Biology, NGS
MISO 0.4.4, 0.4.9 [239] Biology, NGS
MMSEQ 1.0.8 [240] Biology, NGS
MSMBuilder 2.5.1 [241] Molecular Dynamics
MOABS 1.2.9 [242] Biology, NGS, Genomics
Modeller 9.11, 9.13, 9.14 [243] Biology, Modeling
Molden 5.0 [244] Molecular, electronic structure
MolPro 2012.1p22 [245] Quantum Chemistry, Ab Initio
mosaik 2.1.33 [246] Biology,NGS
Mothur 1.31.2 [247] Biology, Microbial Ecology
MOTU 1.1 [248] Biology, Bioinformatics, Genomics
MP-EST 1.4 [249] Biology, Phylogenetics
mpiP 3.4.1 [250] Parallel Computing
MrBayes 3.2.1 [251] Biology, Phylogenetics
MRIcron 201306 [252] Biology, MRI, Imaging
MUMmer 3.23 [253] Biology, Genomics
MUSCLE 3.8.31 [254] Biology, Genomics
MZMine 2.10 [255] Biology, Spectroscopy
NAMD 2.9 [256] Simulation, Chemistry, Biology
Nbody 6 [257] Astronomy
NCBI C++ Toolkit 12.0.0 [258] Biology, C++, Development
NCL 6.1.2 [259] Atmosphere Science
NCO 4.2.1, 4.4.3 [260] Data exchange tools
Ncview 2.1.2 [261] Data visualization
NetCDF 3.4.2, 4.2, 4.3 [262] Data exchange, Tools
Newbler 2.6, 2.7 [263] Biology, NGS
Nextallele 20140718 [264] Biology, Genomics
Nexus NCL 2.1.18 [265] Biology, Phylogenetics, Library
ngsCAT 0.1 [266] Biology, Bioinformatics, NGS
NGSUtils 20130722 [267] Biology, NGS
Nipype 0.10.0 [268] Biology, Bioinformatics, Neuroscience, Imaging
NMRPipe 7.9 [269] Biology, Biochemistry
Novoalign 2.08.02, 3.00.02 [270] Biology, NGS
Oases 0.2.08 [271] Biology, NGS
Olego 1.1.2, 1.1.5 [272] Biology, NGS, RNA-Seq
Octave 3.6.4 [273] Numerical Computation
OpenBabel 2.3.2 [274] Biology, Chemistry
OpenCL 1.1 [275] Programming, Library
OpenCV 2.4.8 [276] Computervision
OpenFOAM 2.1.1 [277] Fluid Dynamics
OpenMM 6.2.0 [278] Quantum Chemistry
OrthoMCL 2.0.2, 2.0.3, 2.0.7 [279] Biology, Genomics
p4vasp 0.3.29 [280] Molecular, Electronic Structure
Pacbio 2.2.0.133377 [281] Biology, Bioinformatics, NGS
PALES 122 [282] Physics
PAML 4.7, 4.8a [283] Biology, Phylogenetics
Pandaseq 20140808 [284] Biology, Bioinformatics, NGS, Sequencing
PAPI 5.1.0.2 [285] Software, Computing
Parallel 20150122 [286] Programming, Languages
ParaView 4.1.0 [287] Data Analysis
PartitionFinder 1.0.1, 1.1.1 [288] Biology, Phylogenetics, Evolution
Parflow v615 [289] Ecology, Modeling
PASA 1.5, 2.0-r20130605p1, 2.0-r20130907 [290] Biology, Genomics
PAUP 4.0b10 [291] Biology, Phylogenetics
PBJelly 14.7.14 [292] Biology, Bioinformatics
pbsdrmaa 1.0.17 [293] Libraries, Torque
PeakSplitter 1.0 [294] Biology, Chip-Seq
PEAR 0.9.2, 0.9.6 [295] Biology, NGS
PDT 3.18 [296] Programming, Profiler
Perl 5.16.0 [297] Programming, Language
PerM 0.4.0 [298] Biology, NGS
PETSc 2.3, 3.3 [299] Math, Numerical solvers
Phenix 1.8.1069 [300] Crystallography
PfamScan 1.3 [301] Biology, Genomics
PHITS 2.52 [302] Physics
Phonopy 1.9.2 [303] Chemistry
PhyloBayes 3.3f, 1.4f MPI [304] Biology, Phylogenetics
Phylosift 1.1 [305] Biology, Genomics, Phylogenetics, Taxonomy
PhyML 3.0, 20121109 [306] Biology, Phylogenetics
Picard 1.69, 1.72, 1.80 [307] Biology, NGS
PLAST 1.0 [308] Biology, Bioinformatics
Plink 1.07 [309] Biology, GWAS
PLINKSEQ 0.10 [310] Biology, Genomics
PluMiST 1.1 [311] Biology, Phylogenetics, Genomics
Preseq 0.0.4 [312] Biology, NGS
Primer3 2.3.4 [313] Biology, Genomics
Prokka 1.10 [314] Biology, Genomics, Bioinformatics, Assembly
ProBABEL 0.4.2, 0.4.3 [315] Biology, Genomics, GWAS
Probalign 1.4 [316] Biology, Genomics
Proovread 1.03rcl [317] Biology, Genomics, NGS
Proteinortho 4.26 [318] Biology, Genomics
python 2.6.8, 2.7.3, 2.7.5, 2.7.6, 2.7.8 [319] Biology, Genomics, NGS
QDD 3.1.2 [320] Programming, scripting, language
QIIME 1.5.0 [321] Biology, Ecology
QT 4.8.3 [322] Computer Science
QUAST 2.3 [323] Biology, NGS
Quickquartet 1.0.0 [324] Biology, Phylogenetics
R 2.15.1, 2.15.0-mpi, Rmpi/2.15.1, 3.0.0, 3.0.1, 3.0.2 [325] Statistics, Programming
R8S 1.71 [326] Biology, Evolution
RADICAL 0.2 [327] Biology, Phylogenetics, Genomics
RAxML 7.9.1, 8.0.25, 8.1.12 [328] Biology, Phylogenetics
RepeatMasker 3.3.0 [329] Biology, Genomics
Reptile 1.1 [330] Biology, NGS, error correction
riboPicker 0.4.3 [331] Biology, Sequence
RNAhybrid 2.1.1 [332] Biology, Genomics
ROOT 6.0 [333] Data Analysis
Rosetta 2014wk4 [334] Biology, Structure, Modelling
RSEG 0.4.8 [335] Biology, NGS
RSEM 1.1.17, 1.2.7, 1.2.19 [336] Biology, NGS, RNA-Seq
Ruby 1.9.3-p0 [337] Programming, Scripting, Language
Sailfish 0.6.3 [338] Biology, NGS, RNA-Seq
Sambamba 0.5.0-dev, 0.5.1 [339] Biology, NGS
Samstat 1.08 [340] Biology, NGS, Bioinformatics, Sequencing
Samblaster 0.1.14 [341] Biology, NGS
samtools 0.1.16, 0.1.18, 0.1.19, 1.0, 1.1, 1.2 [342] Biology, NGS
SAS 9.3 [343] Statistics, Graphing
SATe 2.2.7 [344] Biology, Phylogenetics
Scalablast 2.4.53, 2.11.5 [345] Biology, Genomics
Scalpel 0.1.1 [346] Biology, NGS
Sharcgs 1.2.11 [347] Biology, NGS, Assembly
Schrodinger 2012, 2013 [348] Simulation, chemistry
SCons 2.3.0 [349] Programming
SCRATCH1D 1.0 [350] Biology, Genomics
Scythe 0.991 [351] Biology, NGS
Segemehl 0.1.9 [352] Biology, NGS, Mapper
SeqPrep 0.5 [353] Biology, NGS
SeqMap 1.0.13 [354] Biology, NGS
Seqtk 20140729 [355] Biology, NGS
SEQuel 1.0.1 [356] Biology, NGS
SeqyClean 1.8.10 [357] Biology, NGS, Bioinformatics
ShoRAH 20131204 [358] Biology, NGS, quality filter
SHRiMP 2.2.3 [359] Biology, NGS
Sickle 1.200, 1.33 [360] Biology, NGS, quality filter
Siesta 2.0.2,3.1 [361] Simulation, Physics, Ab Initio
SIFT 4.0.3b [362] Biology, Genomics
Silo 4.7 [363] Library, Data
SIPeS 2.0 [364] Biology, Bioinformatics, ChIP-Seq
Slicer 4.3.1 [365] Biology, Imaging
SMALT 0.7.6 [366] Biology, NGS
Snap 20100728 [367] Biology, Genomics
SnpEff 3.3h, 4.0e [368] Biology, NGS, Genomics
SOAPdenovo 1.05 [369] Biology, NGS
SOAPdenovo-Trans 1.01, 1.03 [370] Biology, NGS
SOAPsplice 1.10 [371] Biology, NGS
SparCC 201402 [372] Microbial Ecology
Spades 2.5.0, 2.5.1, 3.0.0, 3.1.0, 3.5.0 [373] Biology, NGS
Spanki 0.4.1, 0.4.3 [374] Biology, NGS, RNA-Seq
SPARTA+ 2.60 [375] Chemistry
SPIMAP 1.1 [376] Biology, Phylogenetics
SpliceTrap 0.90.5 [377] Biology, NGS, RNA-Seq
SPM 8 [378] Biology, Statistics, Neurology, Imaging
Sputnik 1.0 [379] Biology, Genomics
SQLite 3.8.8.2 [380] Database
SRA 2.1.10 [381]] biology, NGS
SSPACE 2.0 [382] Biology, NGS
Stacks 0.9995 [383] Biology, Genomics, NGS
STAR 2.3.0e [384] Biology, NGS, Alignment
STAR-CCM+ 8.06 [385] Mechanical Engineering
Stata 10.1, 13 [386] Statistics, Data analysis
Stringtie 0.97 [387] Biology, NGS, Alignment
Structure 2.3.3, 2.3.4 [388] Biology, Population
SUNDIALS 2.3.0, 2.5.0 [389] Numerical Solver
SVDetect 0.8b [390] Biology, NGS, SNP
swak4Foam 2.x [391] Fluid Dynamics
swarm 1.2.11 [392] Data Analysis
Swig 2.0.9 [393] Programming, C, C++, Python
SwitchSeq 20140907 [394] Biology, NGS
Syzygy 1.2.7 [395] Biology, Genomics
TASSEL 5.0 [396] Biology, Genomics
TAU 2.21.4, 2.23 [397] Profiling, Tracing, Programming
T-Coffee 9.03.r1318 [398] Biology, Genomics, Multiple Alignment
TESS 2.3.1 [399] Biology, Genomics, Markov
tgicl 2.1 [400] Biology, sequencing, clustering
TomoPy 0.0.3 [401] Biology, Neuroimaging
Tophat 1.4.1, 2.0.13 [402] Biology, NGS
Totalview 8.12.0 [403] Computer Science
TPP 4.7.0 [404] Bioinformatics, MassSpec
TrackTools 2011 [405] Bioinformatics
TrackVis 0.5.2.2 [406] Biology, Spectroscopy
Tracula 5.3.2014_05_26 [407] Biology, Bioinformatics, Neuroscience, Imaging
TraitRate 1.1 [408] Biology, Evolution
TransDecoder 20140704 [409] Biology, NGS
TreeFix 1.1.7 [410] Biology, Phylogenetics
TRF 4.04 [411] Biology, Genomics
Trilinos 11.4.1, 11.8.1 [412] Math Algorithm
Trim Galore 0.2.8 [413] Biology, NGS
Trimmomatic 0.22, 0.32 [414] Biology, NGS
Trinity r20131110, r20140413, r20150215-2.0.4 [415] Biology, NGS, RNA-Seq
TRNAscan-SE 1.23 [416] Biology, NGS, Bioinformatics
Twinscan 4.1.2 [417] Biology, Genomics
usearch 7.0.1001-64, 8.0.1517 [418] Biology, Sequence analysis
UDUNITS 2.2.17 [419] Library, Units, Programming
UNAFold 3.8 [420] Biology, Genome, RNA, Folding
Valgrind 3.9.0 [421] Computer Science
VASP 4.6.34, 5.2.12, 5.3.2, 5.3.3, 5.3.5 [422] Quantum Chemistry, Ab Initio
VarScan 2.3.6 [423] Biology, NGS, Genomics
VCFLib 20121207 [424] Biology, NGS, Genomics
VCFtools 0.1.9, 0.1.10 [425] Biology, SNPs
velvet 1.2.06, 1.2.07, 1.2.10 [426] Biology, Genomics, NGS
VEP 74 [427] Biology, NGS
Vim 7.4.5-minimal, 7.4.5-py2, 7.4.5 [428] Programming, Scripting, Language
vmd 1.9.1 [429] Biology, Visualization
VTK 6.1.0 [430] Visualization, Graphics
Wannier90 1.2, 2.0.0 [431] Computational Physics
WebLogo 3.3 [432] Biology, Genomics
WDSSII 1 [433] Meteorology
WIEN2k 12.1 [434] Material Science, Chemistry
Wgs or Celera 8.1, 8.2, 8.3rc1 [435] Biology, NGS
wublast 2.0 [436] Biology, Sequence Alignment
YAHA 0.1.82 [437] Biology NGS
XCrySDen 1.5.60 [438] Computational Material Science
Yambo 3.3.0 [439] Physics
Yasra 2.32 [440] 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=13343"