Difference between revisions of "Installed Software"

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| [[Gaussian]] || E01, G03, G09-A.02, G09-C.01 || [http://www.gaussian.com/]||Modeling, Computational Chemistry
 
| [[Gaussian]] || E01, G03, G09-A.02, G09-C.01 || [http://www.gaussian.com/]||Modeling, Computational Chemistry
 
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<!-- | [[Geneid]] || 1.4 || [http://genome.crg.es/software/geneid/]||Biology, Genomics, Annotation|| X ||
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<!-- | [[Geneid]] || 1.4 || [http://genome.crg.es/software/geneid/]||Biology, Genomics, Annotation|| -->
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| [[GEMINI]] || 4.6.0a || [https://github.com/arq5x/gemini] || Biology, Genomics, Genetics
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| [[GeneMark]] || 2012.04 || [http://exon.gatech.edu/] || Biology, Genomics, Metagenomics
 
| [[GeneMark]] || 2012.04 || [http://exon.gatech.edu/] || Biology, Genomics, Metagenomics
 
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Revision as of 02:47, 23 November 2013

Installed Software List

Last updated 2013-11-23.

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

Name Version [1] Website Category
AbInit 6.12.3 [1] Ab Initio Quantum Chemistry, Density Functional Theory
Abyss 1.3.3, 1.3.4, 1.3.4-mpi [2] Biology, NGS
ALLPATHS-LG 42316, 44837 [3] Biology, NGS
AFNI 2011_12_21_1014 [4] Biology, Statistics, Imaging, Neurology
Amber 11, 12 [5] Simulation, chemistry
AMOS 3.1.0 [6] Biology, Genomics, NGS
ANNOVAR 20120621,20121023,20130321 [7] Biology, Genomics
Amuse 6.0 [8] Astrophysics
Affymetrix Power Tools 1.15.0 [9] Biology, Genomics, Microarray
Augustus 2.6 [10] Biology, NGS
BamBam 1.0 [11] Biology, NGS
Bamtools 2.1.1 [12] Biology, NGS
BamUtil 1.0.2 [13] Biology, NGS
BayesRate 1.3.43 [14] Biology, Phylogenetics
Bbcp 12.08.17.00.0 [15] Network file transfer
BEAGLE 3.2.2 [16] Biology, Genetics, Genotyping
BEAST 1.7.5, 2.0.1, 2.0.2.pre [17] Biology, Phylogenetics
BEDTools 2.16.2 [18] Biology, NGS
BEST 2.3 [19] Biology, Phylogenetics
BFAST 0.7.0 [20] Biology, NGS
Bismark 0.7.4, 0.7.7 [21] Biology, Methylation, NGS
Bioconductor Latest [22] Biology, R, Statistics
BioPerl 1.006901 [23] Biology, Perl
BioPython 1.59 [24] Biology, Python
BLASR 20130815 [25] Biology, NGS
NCBI BLAST 2.2.26, 2.2.27, 2.2.28 [26] Biology, Sequence alignment
Blast2go 2.5.0-20120705 [27] Biology, Annotation
BLAT 20120524 [28] Biology, Sequence alignment
Boost 1.49.0, 1.53.0, 1.54.0 [29] C++, Library
Bwa 0.6.1, 0.7.2 [30] Biology, NGS
Bowtie 0.12.8, 0.12.9, 2.1.0 [31] Biology, NGS
CAP3 20120705 [32] Biology, sequence assembly
CASAVA 1.8.2 [33] Biology, NGS
CD-HIT 4.6 [34] Biology, Genomics
CDO 1.6.1 [35] Climate
CellProfiler 2.0 [36] Biology, Image Analysis
Charmm 36a3 [37] Simulation, Chemistry
Circos 0.63-pre11 [38] Biology, Visualization
CisGenome 2.0 [39] Biology, Genomics, Peak Calling
ClustalW 2.1 [40] Biology, Genomics
Clview 20130402 [41] Biology, Genomics
CMake 2.8.8 [42] Programming, Build System
Consed 23.0 [43] Biology, Genomics
CUDA 4.2, 5.5 [44] Programming, Graphics
Cufflinks 1.3.0, 2.0.0, 2.0.2 [45] Biology, NGS
Cutadapt 1.1 [46] Biology, NGS
Desmond 3.0.3.1 [47] Simulation, Biology, Chemistry
Dalton 2011 [48] Quantum Chemistry
Dindel 1.01 [49] Biology, NGS
DIYABC many [50] Biology, Genomics
Dlpoly 4.03.4 [51] Simulation, Biology, Chemistry
DNA Clust 3.0 [52] Biology, Genomics
Dock 6.5, 6.6 [53] Chemistry, ligand binding prediction
DTI-TK 2.3.1 [54] Biology, Neurology, Imaging
EIGENSOFT 4.2, 5.0.1 [55] Biology, Population
emboss 6.5.7 [56] Biology, multi-tool suite
Espresso 5.0.1 [57] Modeling, Physics
ESPRIT 201211 [58] Biology, NGS, Metagenomics
ETE2 2.1 [59] Biology, Phylogenetics
Eval 2.2.8 [60] Biology, Genomics, GUI
ExaML 20130314 [61] Biology, Phylogenetics
Exonerate 2.2.0 [62] Biology, Genomics
FAR 2.15 [63] Biology, Genomics
FASTA 34.26.5 [64] Biology, Genomics
FastML 3.0 [65] Biology, Phylogenetics, ML
FastQC 0.9.6, 0.10.1 [66] Biology, NGS
Fastx_toolkit 0.0.13.2 [67] Biology, NGS
Ferret 6.82 [68] Oceanography, Meteorology
FFTW 3.3.2, 3.3.3 [69] Math, Library, C++
Fluent 14.5.7 [70] Simulation, Fluid Dynamics
FragGeneScan 1.16 [71] Biology, NGS, Genomics
FreeBayes 0.9.6 [72] Biology, NGS, SNP Calling
FSL 5.0.2.2 [73] Biology, Neurology, Imaging
Garli 2.0 [74] Biology, Phylogenetics
GATK 1.6.9, 2.2.15, 2.6.5 [75] Biology, NGS
Gaussian E01, G03, G09-A.02, G09-C.01 [76] Modeling, Computational Chemistry
GEMINI 4.6.0a [77] Biology, Genomics, Genetics
GeneMark 2012.04 [78] Biology, Genomics, Metagenomics
Genewise 2.2.0 [79] Biology, Genomics, Annotation
GenomicTools 2.7.0 [80] Biology, NGS
Git 1.8.2.1 [81] Development, Revision Control
Gmap 20120712, 20130331, 20130618 [82] Biology, Genomics
GnuPlot 4.6.0 [83] Graphics, Plotting, Programming
Grace 5.1.22 [84] Graphics, plotting, 2D
GrADS 2.0.1 [85] Earth Science
Gromacs 4.5.5 [86] Chemistry, Modeling, Simulation
GSL 1.15 [87] Library, Math, C++, C
GULP 4.0 [88] Material Science
HaMStR v8b [89] Biology, Genomics
HDF5 1.8.9 [90] Library, Data
HMMER3 3.0 [91] Biology, Genomics
HOMER 4.2 [92] Biology, Genomics
HTSeq 0.5.3p3 [93] Biology, NGS
HyPhy 2.1.2.28 [94] Biology, Phylogenetics
Hypre 2.8.0b [95] Library, Math, Physics
IDBA-UD 1.0.9, 1.1.0 [96] Biology, NGS
IM and IMa 20091217 [97] Biology, Population
IMa2 20120827 [98] Biology, Population
Intel Compilers 11.1, 2012 [99] Programming, Compilers
IOAPI 3.1 [100] Meteorology
Iprscan 4.8 [101] Biology, Genomics
LS-DYNA 610 [102] Physics
ITK 4.3.1 [103] Biology, Genomics
JAGS 3.3.0 [104] Statistics
Java 1.6.0_31, 1.7.0_02 [105] Java Development Kit
Kent 20120524 [106] Biology, NGS
Kmer 1934 [107] Biology, NGS
LAMMPS 28Oct12, 30Sep13 [108] Molecular Dynamics Simulation
Last 193, 247 [109] Biology, Sequence alignment
Lastz 1.03.02, 1.02.00 [110] Biology, NGS
LIBSVM 3.12 [111] Machine Learning
LSC 0.3 [112] Biology, NGS, Error correction
MACH 1.0.18 [113] Biology, Genomics
MACS 1.4.2 [114] Biology, ChIP-Seq
mafft 7.037, 6.903 [115] Biology, Multiple sequence alignment
Maker 2.10, 2.25b [116] Biology, Annotation, Genomics
Maq 0.7.1 [117] Biology, NGS
Matlab 2012a [118] Math, Simulation, Programming
MATS 2.1.0, 3.0.6b, 3.0.8 [119] BIology, NGS
Mauve 2.3.1 [120] Biology, Genomics, Multiple genome alignments
MCNP 5, 6b2 [121] Physics
MCNPX 2.7.0, 2.7.0-i8 [122] Physics
Meme 4.8.1 [123] Biology, Motifs, Sequence analysis
Mercurial 2.7 [124] Development, Revision Control
Metabin 1.0 [125] Biology, Metagenomics
MetaCluster 5.0beta [126] Biology, Metagenomics
MetaVelvet 1.2.01 [127] Biology, NGS
MetaGeneMark 2012.04 [128] Biology, Genomics
Mfold 3.6 [129] Biology, Genomics
Midnight Commander 4.6.1 [130] Tools, Utilities
Migrate-n 3.3.0 [131] Biology, Population
mira 3.2.0, 3.4.0.1, 3.9.9, 3.9.18, 4.0.rc1 [132] Biology, NGS
MISO 0.4.4 [133] Biology, NGS
MSMBuilder 2.5.1 [134] Molecular Dynamics
Molden 5.0 [135] Molecular, electronic structure
mosaik 2.1.33 [136] Biology,NGS
Mothur 1.31.2 [137] Biology, Microbial Ecology
MrBayes 3.2.1 [138] Biology, Phylogenetics
MUMmer 3.23 [139] Biology, Genomics
MUSCLE 3.8.31 [140] Biology, Genomics
NAMD 2.9 [141] Simulation, Chemistry, Biology
Nbody 6 [142] Astronomy
NCO 4.2.1 [143] Data exchange tools
NetCDF 4.2 [144] Data exchange, Tools
Newbler 2.6, 2.7 [145] Biology, NGS
NMRPipe 7.9 [146] Biology, Biochemistry
Novoalign 2.08.02, 3.00.02 [147] Biology, NGS
Oases 0.2.08 [148] Biology, NGS
Olego 1.1.2 [149] Biology, NGS, RNA-Seq
Octave 3.6.4 [150] Numerical Computation
OpenBabel 2.3.2 [151] Biology, Chemistry
OpenFOAM 2.1.1 [152] Fluid Dynamics
OrthoMCL 2.0.2, 2.0.3, 2.0.7 [153] Biology, Genomics
PAML 4.7 [154] Biology, Phylogenetics
PartitionFinder 1.0.1 [155] Biology, Phylogenetics, Evolution
Parflow v615 [156] Ecology, Modeling
PASA 1.5, 2.0-r20130605p1, 2.0-r20130907 [157] Biology, Genomics
PeakSplitter 1.0 [158] Biology, Chip-Seq
PDT 3.18 [159] Programming, Profiler
Perl 5.16.0 [160] Programming, Language
PerM 0.4.0 [161] Biology, NGS
PETSc 2.3, 3.3 [162] Math, Numerical solvers
Phenix 1.8.1069 [163] Crystallography
PHITS 2.52 [164] Physics
PhyloBayes 3.3f, 1.4f MPI [165] Biology, Phylogenetics
PhyML 3.0, 20121109 [166] Biology, Phylogenetics
Picard 1.69, 1.72, 1.80 [167] Biology, NGS
Preseq 0.0.4 [168] Biology, NGS
Proteinortho 4.26 [169] Biology, Genomics
python 2.6.8, 2.7.3 [170] Programming, scripting, language
QIIME 1.5.0 [171] Biology, Ecology
QT 4.8.3 [172] Computer Science
R 2.15.1, 2.15.0-mpi, Rmpi/2.15.1, 3.0.0 [173] Statistics, Programming
R8S 1.71 [174] Biology, Evolution
RADICAL 0.2 [175] Biology, Phylogenetics, Genomics
RAxML 7.3.2.0705, 7.9.1 [176] Biology, Phylogenetics
RepeatMasker 3.3.0 [177] Biology, Genomics
Reptile 1.1 [178] Biology, NGS, error correction
riboPicker 0.4.3 [179] Biology, Sequence
RSEG 0.4.8 [180] Biology, NGS
samtools 0.1.16, 0.1.18, 0.1.19 [181] Biology, NGS
SAS 9.3 [182] Statistics, Graphing
SATe 2.2.7 [183] Biology, Phylogenetics
Sharcgs 1.2.11 [184] Biology, NGS, de novo assembly
Schrodinger 2012, 2013 [185] Simulation, chemistry
SCons 2.3.0 [186] Programming, Build System
SeqPrep 0.5 [187] Biology, NGS
SEQuel 1.0.1 [188] Biology, NGS
Sickle 1.200 [189] Biology, NGS, quality filter
Siesta 2.0.2,3.1 [190] Simulation, Physics, Ab Initio
SIFT 4.0.3b [191] Biology, Genomics
Silo 4.7 [192] Library, Data
Snap 20100728 [193] Biology, Genomics
SOAPdenovo 1.05 [194] Biology, NGS
SOAPdenovo-Trans 1.01 [195] Biology, NGS
Spades 2.5.0, 2.5.1 [196] Biology, NGS
Spanki 0.4.1 [197] Biology, NGS, RNA-Seq
SPARTA+ 2.60 [198] Chemistry
SPIMAP 1.1 [199] Biology, Phylogenetics
SpliceTrap 0.90.5 [200] Biology, NGS, RNA-Seq
SPM 8 [201] Biology, Statistics, Neurology, Imaging
Sputnik 1.0 [202] Biology, Genomics
SRA 2.1.10 [203]] biology, NGS
SSPACE 2.0 [204] Biology, NGS
Stacks 0.9995 [205] Biology, Genomics, NGS
Stata 10.1 [206] Statistics, Data analysis
Structure 2.3.3, 2.3.4 [207] Biology, Population
SUNDIALS 2.5.0 [208] Numerical Solver
swak4Foam 2.x [209] Fluid Dynamics
Swig 2.0.9 [210] Programming, C, C++, Python
TAU 2.21.4 [211] Profiling, Tracing, Programming
T-Coffee 9.03.r1318 [212] Biology, Genomics, Multiple Alignment
tgicl 2.1 [213] Biology, sequencing, clustering
Tophat 1.4.1, 2.0.1, 2.0.8b [214] Biology, NGS
TreeFix 1.1.7 [215] Biology, Phylogenetics
TRF 4.04 [216] Biology, Genomics
Trilinos 11.4.1 [217] Math Algorithm
Trimmomatic 0.22 [218] Biology, NGS
Trinity r20120905, r20121005, r20120225 [219] Biology, NGS, RNA-Seq
Twinscan 4.1.2 [220] Biology, Genomics
usearch 5.2.32, 7.0.959, 7.0.1001-64 (licensed 64-bit) [221] Biology, Sequence analysis
Valgrind 3.9.0 [222] Computer Science
VASP 4.6.34, 5.2.12, 5.3.2 [223] Quantum Chemistry, Ab Initio
VCFtools 0.1.9, 0.1.10 [224] Biology, SNPs
velvet 1.2.06, 1.2.07, 1.2.10 [225] Biology, NGS
vmd 1.9.1 [226] Biology, Visualization
WebLogo 3.3 [227] Biology, Genomics
WDSSII 1 [228] Meteorology
WIEN2k 12.1 [229] Material Science, Chemistry
wgs 7.0.1.22 [230] Biology, NGS
wublast 2.0 [231] Biology, Sequence Alignment
Yambo 3.3.0 [232] Physics
Yasra 2.32 [233] 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=11856"