Difference between revisions of "Installed Software"

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Line 245: Line 245:
 
| [[HaMStR]] || v8b || [http://www.deep-phylogeny.org/hamstr/] || Biology, Genomics
 
| [[HaMStR]] || v8b || [http://www.deep-phylogeny.org/hamstr/] || Biology, Genomics
 
|-
 
|-
−
| [[HDF5]] || 1.8.9 || [http://www.hdfgroup.org/HDF5/]||Library, Data
+
| [[HDF5]] || '''1.8.9''', 1.8.12|| [http://www.hdfgroup.org/HDF5/]||Library, Data
 
|-
 
|-
 
| [[HMMER3]] || 3.0 || [http://hmmer.janelia.org/]||Biology, Genomics
 
| [[HMMER3]] || 3.0 || [http://hmmer.janelia.org/]||Biology, Genomics

Revision as of 17:31, 18 February 2014

Installed Software List

Last updated 2014-02-18.

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
AtomEye 3 [10] Material Science
Augustus 2.6 [11] Biology, NGS
BamBam 1.0 [12] Biology, NGS
Bamtools 2.1.1 [13] Biology, NGS
BamUtil 1.0.2 [14] Biology, NGS
BayesRate 1.3.43 [15] Biology, Phylogenetics
Bbcp 12.08.17.00.0 [16] Network file transfer
BEAGLE 3.2.2 [17] Biology, Genetics, Genotyping
BEAST 1.7.5, 2.0.1, 2.0.2.pre [18] Biology, Phylogenetics
BEDTools 2.16.2, 2.17.0 [19] Biology, NGS
BEST 2.3 [20] Biology, Phylogenetics
BETA 1.0.5 [21] Biology, NGS
BFAST 0.7.0 [22] Biology, NGS
Bismark 0.7.4, 0.7.7 [23] Biology, Methylation, NGS
Bioconductor Latest [24] Biology, R, Statistics
BioPerl 1.006901 [25] Biology, Perl
BioPython 1.59 [26] Biology, Python
BLASR 20130815 [27] Biology, NGS
NCBI BLAST 2.2.27, 2.2.28, 2.2.29 [28] Biology, Sequence alignment
Blast2go 2.5.0-20120705 [29] Biology, Annotation
BLAT 20120524 [30] Biology, Sequence alignment
Boost 1.49.0, 1.53.0, 1.54.0 [31] C++, Library
Bwa 0.6.1, 0.7.2, 0.7.6a [32] Biology, NGS
Bowtie 0.12.8, 0.12.9, 2.1.0 [33] Biology, NGS
CAP3 20120705 [34] Biology, sequence assembly
CASAVA 1.8.2 [35] Biology, NGS
CD-HIT 4.6 [36] Biology, Genomics
CDO 1.6.1 [37] Climate
CellProfiler 2.0 [38] Biology, Image Analysis
Charmm 36a3 [39] Simulation, Chemistry
Circos 0.63-pre11 [40] Biology, Visualization
CisGenome 2.0 [41] Biology, Genomics, Peak Calling
ClustalW 2.1 [42] Biology, Genomics
Clview 20130402 [43] Biology, Genomics
CMake 2.8.8 [44] Programming, Build System
Consed 23.0 [45] Biology, Genomics
CUDA 4.2, 5.5 [46] Programming, Graphics
Cufflinks 1.3.0, 2.0.0, 2.0.2 [47] Biology, NGS
Cutadapt 1.1 [48] Biology, NGS
DDSCAT 7.3.0 [49] Astrophysics
Desmond 3.0.3.1 [50] Simulation, Biology, Chemistry
Dalton 2011 [51] Quantum Chemistry
DiffReps 1.55.4 [52] Biology, NGS, ChIP-Seq
Dindel 1.01 [53] Biology, NGS
DIYABC many [54] Biology, Genomics
Dlpoly 4.03.4 [55] Simulation, Biology, Chemistry
DNA Clust 3.0 [56] Biology, Genomics
Dock 6.5, 6.6 [57] Chemistry, ligand binding prediction
DTI-TK 2.3.1 [58] Biology, Neurology, Imaging
EIGENSOFT 4.2, 5.0.1 [59] Biology, Population
emboss 6.5.7 [60] Biology, multi-tool suite
Espresso 5.0.1 [61] Modeling, Physics
ESPRIT 201211 [62] Biology, NGS, Metagenomics
ETE2 2.1 [63] Biology, Phylogenetics
Eval 2.2.8 [64] Biology, Genomics, GUI
ExaML 20130314 [65] Biology, Phylogenetics
Exonerate 2.2.0 [66] Biology, Genomics
FAR 2.15 [67] Biology, Genomics
FASTA 34.26.5, 36.3.6d [68] Biology, Genomics
FastML 3.0 [69] Biology, Phylogenetics, ML
FastQC 0.9.6, 0.10.1 [70] Biology, NGS
Fastx_toolkit 0.0.13.2 [71] Biology, NGS
fcGENE 1.0.7 [72] Biology, Genomics, SNP
Ferret 6.82 [73] Oceanography, Meteorology
FFTW 3.3.2, 3.3.3 [74] Math, Library, C++
Fluent 14.5.7 [75] Simulation, Fluid Dynamics
FragGeneScan 1.16 [76] Biology, NGS, Genomics
FreeBayes 0.9.6 [77] Biology, NGS, SNP Calling
FSL 5.0.2.2 [78] Biology, Neurology, Imaging
Garli 2.0, 2.01 [79] Biology, Phylogenetics
GATK 1.6.9, 2.2.15, 2.6.5 [80] Biology, NGS
Gaussian E01, G03, G09-A.02, G09-C.01 [81] Modeling, Computational Chemistry
GEMINI 4.6.0a [82] Biology, Genomics, Genetics
GenBank Tools 20140130 [83] BIology< Genomics
GeneMark 2012.04 [84] Biology, Genomics, Metagenomics
Genewise 2.2.0 [85] Biology, Genomics, Annotation
GenomicTools 2.7.0 [86] Biology, NGS
Git 1.8.2.1 [87] Development, Revision Control
Gmap 20120712, 20130331, 20130618 [88] Biology, Genomics
GnuPlot 4.6.0 [89] Graphics, Plotting, Programming
Grace 5.1.22 [90] Graphics, plotting, 2D
GrADS 2.0.1 [91] Earth Science
Gromacs 4.5.5, 4.6.5 [92] Chemistry, Modeling, Simulation
GSL 1.15 [93] Library, Math, C++, C
GULP 4.0 [94] Material Science
HaMStR v8b [95] Biology, Genomics
HDF5 1.8.9, 1.8.12 [96] Library, Data
HMMER3 3.0 [97] Biology, Genomics
HOMER 4.2 [98] Biology, Genomics
HTSeq 0.5.3p3 [99] Biology, NGS
HyPhy 2.1.2.28 [100] Biology, Phylogenetics
Hypre 2.8.0b [101] Library, Math, Physics
IDBA-UD 1.0.9, 1.1.0 [102] Biology, NGS
IM and IMa 20091217 [103] Biology, Population
IMa2 20120827 [104] Biology, Population
Intel Compilers 11.1, 2012 [105] Programming, Compilers
IOAPI 3.1 [106] Meteorology
Iprscan 4.8 [107] Biology, Genomics
LS-DYNA 700 [108] Physics
ITK 4.3.1 [109] Biology, Genomics
JAGS 3.3.0 [110] Statistics
Java 1.6.0_31, 1.7.0_02 [111] Java Development Kit
Kent 20120524 [112] Biology, NGS
Kmer 1934 [113] Biology, NGS
LAMMPS 28Oct12, 30Sep13 [114] Molecular Dynamics Simulation
Last 193, 247 [115] Biology, Sequence alignment
Lastz 1.03.02, 1.02.00 [116] Biology, NGS
LIBSVM 3.12 [117] Machine Learning
LSC 0.3, 0.3.1 [118] Biology, NGS, Error correction
MACH 1.0.18 [119] Biology, Genomics
MACS 1.4.2 [120] Biology, ChIP-Seq
mafft 7.037, 6.903 [121] Biology, Multiple sequence alignment
Maker 2.10, 2.25b [122] Biology, Annotation, Genomics
Maq 0.7.1 [123] Biology, NGS
Matlab 2012a [124] Math, Simulation, Programming
MATS 2.1.0, 3.0.6b, 3.0.8 [125] BIology, NGS
Mauve 2.3.1 [126] Biology, Genomics, Multiple genome alignments
MCNP 5, 6b2 [127] Physics
MCNPX 2.7.0, 2.7.0-i8 [128] Physics
Meme 4.8.1 [129] Biology, Motifs, Sequence analysis
Mercurial 2.7 [130] Development, Revision Control
Metabin 1.0 [131] Biology, Metagenomics
MetaCluster 5.0beta [132] Biology, Metagenomics
MetaVelvet 1.2.01 [133] Biology, NGS
MetaGeneMark 2012.04 [134] Biology, Genomics
Mfold 3.6 [135] Biology, Genomics
Midnight Commander 4.6.1 [136] Tools, Utilities
Migrate-n 3.3.0 [137] Biology, Population
mira 3.2.0, 3.4.0.1, 3.9.9, 3.9.18, 4.0.rc1 [138] Biology, NGS
MISO 0.4.4, 0.4.9 [139] Biology, NGS
MSMBuilder 2.5.1 [140] Molecular Dynamics
Molden 5.0 [141] Molecular, electronic structure
mosaik 2.1.33 [142] Biology,NGS
Mothur 1.31.2 [143] Biology, Microbial Ecology
MrBayes 3.2.1 [144] Biology, Phylogenetics
MUMmer 3.23 [145] Biology, Genomics
MUSCLE 3.8.31 [146] Biology, Genomics
NAMD 2.9 [147] Simulation, Chemistry, Biology
Nbody 6 [148] Astronomy
NCBI C++ Toolkit 12.0.0 [149] Biology, C++, Development
NCL 6.1.2 [150] Atmosphere Science
NCO 4.2.1 [151] Data exchange tools
NetCDF 4.2 [152] Data exchange, Tools
Newbler 2.6, 2.7 [153] Biology, NGS
Nexus NCL 2.1.18 [154] Biology, Phylogenetics, Library
NMRPipe 7.9 [155] Biology, Biochemistry
Novoalign 2.08.02, 3.00.02 [156] Biology, NGS
Oases 0.2.08 [157] Biology, NGS
Olego 1.1.2 [158] Biology, NGS, RNA-Seq
Octave 3.6.4 [159] Numerical Computation
OpenBabel 2.3.2 [160] Biology, Chemistry
OpenFOAM 2.1.1 [161] Fluid Dynamics
OrthoMCL 2.0.2, 2.0.3, 2.0.7 [162] Biology, Genomics
PAML 4.7 [163] Biology, Phylogenetics
PartitionFinder 1.0.1 [164] Biology, Phylogenetics, Evolution
Parflow v615 [165] Ecology, Modeling
PASA 1.5, 2.0-r20130605p1, 2.0-r20130907 [166] Biology, Genomics
PeakSplitter 1.0 [167] Biology, Chip-Seq
PDT 3.18 [168] Programming, Profiler
Perl 5.16.0 [169] Programming, Language
PerM 0.4.0 [170] Biology, NGS
PETSc 2.3, 3.3 [171] Math, Numerical solvers
Phenix 1.8.1069 [172] Crystallography
PHITS 2.52 [173] Physics
PhyloBayes 3.3f, 1.4f MPI [174] Biology, Phylogenetics
PhyML 3.0, 20121109 [175] Biology, Phylogenetics
Picard 1.69, 1.72, 1.80 [176] Biology, NGS
Preseq 0.0.4 [177] Biology, NGS
ProBABEL 0.4.2 [178] Biology, Genomics, GWAS
Proteinortho 4.26 [179] Biology, Genomics
python 2.6.8, 2.7.3 [180] Programming, scripting, language
QIIME 1.5.0 [181] Biology, Ecology
QT 4.8.3 [182] Computer Science
R 2.15.1, 2.15.0-mpi, Rmpi/2.15.1, 3.0.0 [183] Statistics, Programming
R8S 1.71 [184] Biology, Evolution
RADICAL 0.2 [185] Biology, Phylogenetics, Genomics
RAxML 7.3.2.0705, 7.9.1, 8.0.0 [186] Biology, Phylogenetics
RepeatMasker 3.3.0 [187] Biology, Genomics
Reptile 1.1 [188] Biology, NGS, error correction
riboPicker 0.4.3 [189] Biology, Sequence
RSEG 0.4.8 [190] Biology, NGS
samtools 0.1.16, 0.1.18, 0.1.19 [191] Biology, NGS
SAS 9.3 [192] Statistics, Graphing
SATe 2.2.7 [193] Biology, Phylogenetics
Sharcgs 1.2.11 [194] Biology, NGS, de novo assembly
Schrodinger 2012, 2013 [195] Simulation, chemistry
SCons 2.3.0 [196] Programming, Build System
SeqPrep 0.5 [197] Biology, NGS
SEQuel 1.0.1 [198] Biology, NGS
SeqyClean 1.8.10 [199] Biology, NGS, quality filter
Sickle 1.200 [200] Biology, NGS, quality filter
Siesta 2.0.2,3.1 [201] Simulation, Physics, Ab Initio
SIFT 4.0.3b [202] Biology, Genomics
Silo 4.7 [203] Library, Data
Snap 20100728 [204] Biology, Genomics
SOAPdenovo 1.05 [205] Biology, NGS
SOAPdenovo-Trans 1.01 [206] Biology, NGS
SparCC 201402 [207] Microbial Ecology
Spades 2.5.0, 2.5.1, 3.0.0 [208] Biology, NGS
Spanki 0.4.1 [209] Biology, NGS, RNA-Seq
SPARTA+ 2.60 [210] Chemistry
SPIMAP 1.1 [211] Biology, Phylogenetics
SpliceTrap 0.90.5 [212] Biology, NGS, RNA-Seq
SPM 8 [213] Biology, Statistics, Neurology, Imaging
Sputnik 1.0 [214] Biology, Genomics
SRA 2.1.10 [215]] biology, NGS
SSPACE 2.0 [216] Biology, NGS
Stacks 0.9995 [217] Biology, Genomics, NGS
Stata 10.1 [218] Statistics, Data analysis
Structure 2.3.3, 2.3.4 [219] Biology, Population
SUNDIALS 2.5.0 [220] Numerical Solver
swak4Foam 2.x [221] Fluid Dynamics
Swig 2.0.9 [222] Programming, C, C++, Python
TAU 2.21.4 [223] Profiling, Tracing, Programming
T-Coffee 9.03.r1318 [224] Biology, Genomics, Multiple Alignment
tgicl 2.1 [225] Biology, sequencing, clustering
Tophat 1.4.1, 2.0.1, 2.0.8b [226] Biology, NGS
Totalview 8.12.0 [227] Computer Science
TreeFix 1.1.7 [228] Biology, Phylogenetics
TRF 4.04 [229] Biology, Genomics
Trilinos 11.4.1 [230] Math Algorithm
Trimmomatic 0.22 [231] Biology, NGS
Trinity r20120905, r20121005, r20120225 [232] Biology, NGS, RNA-Seq
Twinscan 4.1.2 [233] Biology, Genomics
usearch 5.2.32, 7.0.959, 7.0.1001-64 (licensed 64-bit) [234] Biology, Sequence analysis
Valgrind 3.9.0 [235] Computer Science
VASP 4.6.34, 5.2.12, 5.3.2, 5.3.3 [236] Quantum Chemistry, Ab Initio
VCFtools 0.1.9, 0.1.10 [237] Biology, SNPs
velvet 1.2.06, 1.2.07, 1.2.10 [238] Biology, NGS
vmd 1.9.1 [239] Biology, Visualization
WebLogo 3.3 [240] Biology, Genomics
WDSSII 1 [241] Meteorology
WIEN2k 12.1 [242] Material Science, Chemistry
wgs 7.0.1.22 [243] Biology, NGS
wublast 2.0 [244] Biology, Sequence Alignment
Yambo 3.3.0 [245] Physics
Yasra 2.32 [246] 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=12062"