Difference between revisions of "Installed Software"

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Line 385: Line 385:
 
| [[QIIME]] || 1.5.0 || [http://qiime.org/index.html]|| Biology, Ecology
 
| [[QIIME]] || 1.5.0 || [http://qiime.org/index.html]|| Biology, Ecology
 
|-
 
|-
−
| [[R]] || 2.15.0, 2.15.1, 2.15.0-mpi, Rmpi/2.15.1 || [http://www.r-project.org/] || Statistics, Programming
+
| [[R]] || '''2.15.1''', 2.15.0-mpi, Rmpi/2.15.1, 3.0.0 || [http://www.r-project.org/] || Statistics, Programming
 
|-
 
|-
 
| [[R8S]] || 1.71 || [http://loco.biosci.arizona.edu/r8s/] || Biology, Evolution
 
| [[R8S]] || 1.71 || [http://loco.biosci.arizona.edu/r8s/] || Biology, Evolution

Revision as of 16:01, 11 April 2013

Installed Software List

Last updated 2013-04-11.

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
Amber 11, 12 [4] Simulation, chemistry
Amuse 6.0 [5] Astrophysics
Affymetrix Power Tools 1.15.0 [6] Biology, Genomics, Microarray
Augustus 2.6 [7] Biology, NGS
Bamtools 2.1.1 [8] Biology, NGS
BamUtil 1.0.2 [9] Biology, NGS
BayesRate 1.3.43 [10] Biology, Phylogenetics
Bbcp 12.08.17.00.0 [11] Network file transfer
BEAST 1.7.5, 2.0.1, 2.0.2.pre [12] Biology, Phylogenetics
BEDTools 2.16.2 [13] Biology, NGS
BEST 2.3 [14] Biology, Phylogenetics
BFAST 0.7.0 [15] Biology, NGS
Bismark 0.7.4, 0.7.7 [16] Biology, Methylation, NGS
Bioconductor Latest [17] Biology, R, Statistics
BioPerl 1.006901 [18] Biology, Perl
BioPython 1.59 [19] Biology, Python
NCBI BLAST 2.2.26 (+ and legacy) [20] Biology, Sequence alignment
Blast2go 2.5.0-20120705 [21] Biology, Annotation
BLAT 20120524 [22] Biology, Sequence alignment
Boost 1.49.0 [23] C++, Library
Bwa 0.6.1, 0.7.2 [24] Biology, NGS
Bowtie 0.12.8, 0.12.9, 2.1.0 [25] Biology, NGS
CAP3 20120705 [26] Biology, sequence assembly
CASAVA 1.8.2 [27] Biology, NGS
CD-HIT 4.6 [28] Biology, Genomics
Charmm 36a3 [29] Simulation, Chemistry
Circos 0.63-pre11 [30] Biology, Visualization
CisGenome 2.0 [31] Biology, Genomics, Peak Calling
ClustalW 2.1 [32] Biology, Genomics
CMake 2.8.8 [33] Programming
Consed 23.0 [34] Biology, Genomics
CUDA 4.2 [35] Programming, Graphics
Cufflinks 1.3.0, 2.0.0, 2.0.2 [36] Biology, NGS
Cutadapt 1.1 [37] Biology, NGS
Desmond 3.0.3.1 [38] Simulation, Biology, Chemistry
Dindel 1.01 [39] Biology, NGS
DIYABC many [40] Biology, Genomics
Dlpoly 4.03.4 [41] Simulation, Biology, Chemistry
Dock 6.5, 6.6 [42] Chemistry, ligand binding prediction
emboss 6.5.7 [43] Biology, multi-tool suite
Espresso 5.0.1 [44] Modeling, Physics
ESPRIT 201211 [45] Biology, NGS, Metagenomics
ETE2 2.1 [46] Biology, Phylogenetics
Eval 2.2.8 [47] Biology, Genomics, GUI
ExaML 20130314 [48] Biology, Phylogenetics
Exonerate 2.2.0 [49] Biology, Genomics
FAR 2.15 [50] Biology, Genomics
FASTA 34.26.5 [51] Biology, Genomics
FastQC 0.9.6, 0.10.1 [52] Biology, NGS
Fastx_toolkit 0.0.13.2 [53] Biology, NGS
Ferret 6.82 [54] Oceanography, Meteorology
FFTW 3.3.2 [55] Math, Library, C++
FragGeneScan 1.16 [56] Biology, NGS, Genomics
FreeBayes 0.9.6 [57] Biology
Garli 2.0 [58] Biology, Phylogenetics
GATK 1.6.9 [59] Biology, NGS
Gaussian E01, G03, G09-A.02, G09-C.01 [60] Modeling, Computational Chemistry
GeneMark 2012.04 [61] Biology, Genomics, Metagenomics
Genewise 2.2.0 [62] Biology, Genomics, Annotation
GenomicTools 2.7.0 [63] Biology, NGS
Gmap 20070928, 20120712 [64] Biology, Genomics
GnuPlot 4.6.0 [65] Graphics, Plotting, Programming
Grace 5.1.22 [66] Graphics, plotting, 2D
GrADS 2.0.1 [67] Earth Science
Gromacs 4.5.5 [68] Chemistry, Modeling, Simulation
GSL 1.15 [69] Library, Math, C++, C
HaMStR v8b [70] Biology, Genomics
HDF5 1.8.9 [71] Library, Data
HMMER3 3.0 [72] Biology, Genomics
HTSeq 0.5.3p3 [73] Biology, NGS
HyPhy 2.1.2.28 [74] Biology, Phylogenetics
Hypre 2.8.0b [75] Library, Math, Physics
IDBA-UD 1.0.9, 1.1.0 [76] Biology, NGS
IM and IMa 20091217 [77] Biology, Population
IMa2 20120827 [78] Biology, Population
Intel Compilers 11.1, 2012 [79] Programming, Compilers
Iprscan 4.8 [80] Biology, Genomics
ITK 4.3.1 [81] Biology, Genomics
JDK 1.6.0_31, 1.7.0_02 [82] Java Development Kit
Kent 20120524 [83] Biology, NGS
Kmer 1934 [84] Biology, NGS
LAMMPS 28Oct12 [85] Molecular Dynamics Simulation
Last 193, 247 [86] Biology, Sequence alignment
Lastz 1.03.02, 1.02.00 [87] Biology, NGS
LIBSVM 3.12 [88] Machine Learning
MACS 1.4.2 [89] Biology, ChIP-Seq
mafft 6.903 [90] Biology, Multiple sequence alignment
Maker 2.10, 2.25b [91] Biology, Annotation, Genomics
Maq 0.7.1 [92] Biology, NGS
Matlab 2012a [93] Math, Simulation, Programming
MATS 2.1.0, 3.0.4, 3.0.6 [94] BIology, NGS
MCNP 5, 6b2 [95] Physics
MCNPX 2.7.0, 2.7.0-i8 [96] Physics
Meme 4.8.1 [97] Biology, Motifs, Sequence analysis
MetaCluster 5.0beta [98] Biology
MetaVelvet 1.2.01 [99] Biology, NGS
MetaGeneMark 2012.04 [100] Biology, Genomics
Midnight Commander 4.6.1 [101] Tools, Utilities
Migrate-n 3.3.0 [102] Biology, Population
mira 3.2.0, 3.4.0.1 [103] Biology, NGS
MISO 0.4.4 [104] Biology, NGS
MSMBuilder 2.5.1 [105] Molecular Dynamics
Molden 5.0 [106] Molecular, electronic structure
mosaik 2.1.33 [107] Biology,NGS
MrBayes 3.2.1 [108] Biology, Phylogenetics
MUMmer 3.23 [109] Biology, Genomics
MUSCLE 3.8.31 [110] Biology, Genomics
NAMD 2.9 [111] Simulation, Chemistry, Biology
Nbody 6 [112] Astronomy
NCO 4.2.1 [113] Data exchange tools
NetCDF 4.2 [114] Data exchange, Tools
Newbler 2.6, 2.7 [115] Biology, NGS
Novoalign 2.08.02, 3.00.02 [116] Biology, NGS
Oases 0.2.08 [117] Biology, NGS
Octave 3.6.4 [118] Numerical Computation
OpenFOAM 2.1.1 [119] Fluid Dynamics
OrthoMCL 2.0.2, 2.0.3 [120] Biology, Genomics
PartitionFinder 1.0.1 [121] Biology, Phylogenetics, Evolution
Parflow v615 [122] Ecology, Modeling
PASA 1.5, r20120625 [123] Biology, Genomics
PeakSplitter 1.0 [124] Biology, Chip-Seq
PDT 3.18 [125] Programming, Profiler
Perl 5.16.0 [126] Programming, Language
PerM 0.4.0 [127] Biology, NGS
Phenix 1.8.1069 [128] Crystallography
PhyML 3.0, 20121109 [129] Biology, Phylogenetics
Picard 1.69, 1.72, 1.80 [130] Biology, NGS
Proteinortho 4.26 [131] Biology, Genomics
python 2.6.8, 2.7.3 [132] Programming, scripting, language
QIIME 1.5.0 [133] Biology, Ecology
R 2.15.1, 2.15.0-mpi, Rmpi/2.15.1, 3.0.0 [134] Statistics, Programming
R8S 1.71 [135] Biology, Evolution
RADICAL 0.2 [136] Biology, Phylogenetics, Genomics
RAxML 7.3.2.0705 [137] Biology, Phylogenetics
RepeatMasker 3.3.0 [138] Biology, Genomics
Reptile 1.1 [139] Biology, NGS, error correction
riboPicker 0.4.3 [140] Biology, Sequence
RSEG 0.4.8 [141] Biology, NGS
samtools 0.1.16, 0.1.18, 0.1.19 [142] Biology, NGS
SAS 9.3 [143] Statistics, Graphing
SATe 2.2.7 [144] Biology, Phylogenetics
Schrodinger 2012 [145] Simulation, chemistry
SeqPrep 0.5 [146] Biology, NGS
SEQuel 1.0.1 [147] Biology, NGS
Sickle 1.200 [148] Biology, NGS, quality filter
Siesta 2.0.2,3.1 [149] Simulation, Physics, Ab Initio
SIFT 4.0.3b [150] Biology, Genomics
Silo 4.7 [151] Library, Data
Snap 20100728 [152] Biology, Genomics
SOAPdenovo 1.05 [153] Biology, NGS
SOAPdenovo-Trans 1.01 [154] Biology, NGS
SPARTA+ 2.60 [155] Chemistry
SPIMAP 1.1 [156] Biology, Phylogenetics
SpliceTrap 0.90.5 [157] Biology, NGS, RNA-Seq
Sputnik 1.0 [158] Biology, Genomics
SRA 2.1.10 [159]] biology, NGS
Stacks 0.9995 [160] Biology, Genomics, NGS
Structure 2.3.3 [161] Biology, Population
Swig 2.0.9 [162] Programming, C, C++, Python
TAU 2.21.4 [163] Profiling, Tracing, Programming
tgicl 2.1 [164] Biology, sequencing, clustering
Tophat 1.4.1, 2.0.1 [165] Biology, NGS
TreeFix 1.1.7 [166] Biology, Phylogenetics
TRF 4.04 [167] Biology, Genomics
Trimmomatic 0.22 [168] Biology, NGS
Trinity r20120905, r20121005, r20120225 [169] Biology, RNA-Seq
Twinscan 4.1.2 [170] Biology, Genomics
usearch 5.2.32 [171] Biology, Sequence analysis
VASP 4.6.34, 5.2.12, 5.3.2 [172] Quantum Chemistry, Ab Initio
VCFtools 0.1.9, 0.1.10 [173] Biology, SNPs
velvet 1.2.06, 1.2.07 [174] Biology, NGS
vmd 1.9.1 [175] Biology, Visualization
WebLogo 3.3 [176] Biology, Genomics
WDSSII 1 [177] Meteorology
WIEN2k 12.1 [178] Material Science, Chemistry
wgs 7.0.1.22 [179] Biology, NGS
wublast 2.0 [180] Biology, Sequence Alignment
Yasra 2.32 [181] 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.

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