Difference between revisions of "Installed Software"

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| [[CD-HIT]] || 4.6 || [http://weizhong-lab.ucsd.edu/cd-hit/] || Biology, Genomics
 
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<!-- | [[CEGMA]] || 2.4.010312 || [http://korflab.ucdavis.edu/Datasets/cegma/] || Biology, Genomics, Annotation || X ||-->

Revision as of 20:18, 30 April 2013

Installed Software List

Last updated 2013-04-30.

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
Amuse 6.0 [6] Astrophysics
Affymetrix Power Tools 1.15.0 [7] Biology, Genomics, Microarray
Augustus 2.6 [8] Biology, NGS
Bamtools 2.1.1 [9] Biology, NGS
BamUtil 1.0.2 [10] Biology, NGS
BayesRate 1.3.43 [11] Biology, Phylogenetics
Bbcp 12.08.17.00.0 [12] Network file transfer
BEAST 1.7.5, 2.0.1, 2.0.2.pre [13] Biology, Phylogenetics
BEDTools 2.16.2 [14] Biology, NGS
BEST 2.3 [15] Biology, Phylogenetics
BFAST 0.7.0 [16] Biology, NGS
Bismark 0.7.4, 0.7.7 [17] Biology, Methylation, NGS
Bioconductor Latest [18] Biology, R, Statistics
BioPerl 1.006901 [19] Biology, Perl
BioPython 1.59 [20] Biology, Python
NCBI BLAST 2.2.26 (+ and legacy) [21] Biology, Sequence alignment
Blast2go 2.5.0-20120705 [22] Biology, Annotation
BLAT 20120524 [23] Biology, Sequence alignment
Boost 1.49.0 [24] C++, Library
Bwa 0.6.1, 0.7.2 [25] Biology, NGS
Bowtie 0.12.8, 0.12.9, 2.1.0 [26] Biology, NGS
CAP3 20120705 [27] Biology, sequence assembly
CASAVA 1.8.2 [28] Biology, NGS
CD-HIT 4.6 [29] Biology, Genomics
[[CDO] 1.6.1 [30] Climate
CellProfiler 2.0 [31] Biology, Image Analysis
Charmm 36a3 [32] Simulation, Chemistry
Circos 0.63-pre11 [33] Biology, Visualization
CisGenome 2.0 [34] Biology, Genomics, Peak Calling
ClustalW 2.1 [35] Biology, Genomics
CMake 2.8.8 [36] Programming
Consed 23.0 [37] Biology, Genomics
CUDA 4.2 [38] Programming, Graphics
Cufflinks 1.3.0, 2.0.0, 2.0.2 [39] Biology, NGS
Cutadapt 1.1 [40] Biology, NGS
Desmond 3.0.3.1 [41] Simulation, Biology, Chemistry
Dindel 1.01 [42] Biology, NGS
DIYABC many [43] Biology, Genomics
Dlpoly 4.03.4 [44] Simulation, Biology, Chemistry
Dock 6.5, 6.6 [45] Chemistry, ligand binding prediction
DTI-TK 2.3.1 [46] Bioinformatics, Neurology, Imaging
emboss 6.5.7 [47] Biology, multi-tool suite
Espresso 5.0.1 [48] Modeling, Physics
ESPRIT 201211 [49] Biology, NGS, Metagenomics
ETE2 2.1 [50] Biology, Phylogenetics
Eval 2.2.8 [51] Biology, Genomics, GUI
ExaML 20130314 [52] Biology, Phylogenetics
Exonerate 2.2.0 [53] Biology, Genomics
FAR 2.15 [54] Biology, Genomics
FASTA 34.26.5 [55] Biology, Genomics
FastQC 0.9.6, 0.10.1 [56] Biology, NGS
Fastx_toolkit 0.0.13.2 [57] Biology, NGS
Ferret 6.82 [58] Oceanography, Meteorology
FFTW 3.3.2 [59] Math, Library, C++
FragGeneScan 1.16 [60] Biology, NGS, Genomics
FreeBayes 0.9.6 [61] Biology
FSL 5.0.2.2 [62] Biology, Neurology, Imaging
Garli 2.0 [63] Biology, Phylogenetics
GATK 1.6.9 [64] Biology, NGS
Gaussian E01, G03, G09-A.02, G09-C.01 [65] Modeling, Computational Chemistry
GeneMark 2012.04 [66] Biology, Genomics, Metagenomics
Genewise 2.2.0 [67] Biology, Genomics, Annotation
GenomicTools 2.7.0 [68] Biology, NGS
Gmap 20070928, 20120712 [69] Biology, Genomics
GnuPlot 4.6.0 [70] Graphics, Plotting, Programming
Grace 5.1.22 [71] Graphics, plotting, 2D
GrADS 2.0.1 [72] Earth Science
Gromacs 4.5.5 [73] Chemistry, Modeling, Simulation
GSL 1.15 [74] Library, Math, C++, C
HaMStR v8b [75] Biology, Genomics
HDF5 1.8.9 [76] Library, Data
HMMER3 3.0 [77] Biology, Genomics
HTSeq 0.5.3p3 [78] Biology, NGS
HyPhy 2.1.2.28 [79] Biology, Phylogenetics
Hypre 2.8.0b [80] Library, Math, Physics
IDBA-UD 1.0.9, 1.1.0 [81] Biology, NGS
IM and IMa 20091217 [82] Biology, Population
IMa2 20120827 [83] Biology, Population
Intel Compilers 11.1, 2012 [84] Programming, Compilers
Iprscan 4.8 [85] Biology, Genomics
ITK 4.3.1 [86] Biology, Genomics
JDK 1.6.0_31, 1.7.0_02 [87] Java Development Kit
Kent 20120524 [88] Biology, NGS
Kmer 1934 [89] Biology, NGS
LAMMPS 28Oct12 [90] Molecular Dynamics Simulation
Last 193, 247 [91] Biology, Sequence alignment
Lastz 1.03.02, 1.02.00 [92] Biology, NGS
LIBSVM 3.12 [93] Machine Learning
MACS 1.4.2 [94] Biology, ChIP-Seq
mafft 6.903 [95] Biology, Multiple sequence alignment
Maker 2.10, 2.25b [96] Biology, Annotation, Genomics
Maq 0.7.1 [97] Biology, NGS
Matlab 2012a [98] Math, Simulation, Programming
MATS 2.1.0, 3.0.4, 3.0.6 [99] BIology, NGS
MCNP 5, 6b2 [100] Physics
MCNPX 2.7.0, 2.7.0-i8 [101] Physics
Meme 4.8.1 [102] Biology, Motifs, Sequence analysis
MetaCluster 5.0beta [103] Biology
MetaVelvet 1.2.01 [104] Biology, NGS
MetaGeneMark 2012.04 [105] Biology, Genomics
Midnight Commander 4.6.1 [106] Tools, Utilities
Migrate-n 3.3.0 [107] Biology, Population
mira 3.2.0, 3.4.0.1 [108] Biology, NGS
MISO 0.4.4 [109] Biology, NGS
MSMBuilder 2.5.1 [110] Molecular Dynamics
Molden 5.0 [111] Molecular, electronic structure
mosaik 2.1.33 [112] Biology,NGS
MrBayes 3.2.1 [113] Biology, Phylogenetics
MUMmer 3.23 [114] Biology, Genomics
MUSCLE 3.8.31 [115] Biology, Genomics
NAMD 2.9 [116] Simulation, Chemistry, Biology
Nbody 6 [117] Astronomy
NCO 4.2.1 [118] Data exchange tools
NetCDF 4.2 [119] Data exchange, Tools
Newbler 2.6, 2.7 [120] Biology, NGS
Novoalign 2.08.02, 3.00.02 [121] Biology, NGS
Oases 0.2.08 [122] Biology, NGS
Octave 3.6.4 [123] Numerical Computation
OpenFOAM 2.1.1 [124] Fluid Dynamics
OrthoMCL 2.0.2, 2.0.3, 2.0.7 [125] Biology, Genomics
PartitionFinder 1.0.1 [126] Biology, Phylogenetics, Evolution
Parflow v615 [127] Ecology, Modeling
PASA 1.5, r20120625 [128] Biology, Genomics
PeakSplitter 1.0 [129] Biology, Chip-Seq
PDT 3.18 [130] Programming, Profiler
Perl 5.16.0 [131] Programming, Language
PerM 0.4.0 [132] Biology, NGS
Phenix 1.8.1069 [133] Crystallography
PhyloBayes 3.3f [134] Biology, Phylogenetics
PhyML 3.0, 20121109 [135] Biology, Phylogenetics
Picard 1.69, 1.72, 1.80 [136] Biology, NGS
Proteinortho 4.26 [137] Biology, Genomics
python 2.6.8, 2.7.3 [138] Programming, scripting, language
QIIME 1.5.0 [139] Biology, Ecology
R 2.15.1, 2.15.0-mpi, Rmpi/2.15.1, 3.0.0 [140] Statistics, Programming
R8S 1.71 [141] Biology, Evolution
RADICAL 0.2 [142] Biology, Phylogenetics, Genomics
RAxML 7.3.2.0705 [143] Biology, Phylogenetics
RepeatMasker 3.3.0 [144] Biology, Genomics
Reptile 1.1 [145] Biology, NGS, error correction
riboPicker 0.4.3 [146] Biology, Sequence
RSEG 0.4.8 [147] Biology, NGS
samtools 0.1.16, 0.1.18, 0.1.19 [148] Biology, NGS
SAS 9.3 [149] Statistics, Graphing
SATe 2.2.7 [150] Biology, Phylogenetics
Schrodinger 2012 [151] Simulation, chemistry
SeqPrep 0.5 [152] Biology, NGS
SEQuel 1.0.1 [153] Biology, NGS
Sickle 1.200 [154] Biology, NGS, quality filter
Siesta 2.0.2,3.1 [155] Simulation, Physics, Ab Initio
SIFT 4.0.3b [156] Biology, Genomics
Silo 4.7 [157] Library, Data
Snap 20100728 [158] Biology, Genomics
SOAPdenovo 1.05 [159] Biology, NGS
SOAPdenovo-Trans 1.01 [160] Biology, NGS
SPARTA+ 2.60 [161] Chemistry
SPIMAP 1.1 [162] Biology, Phylogenetics
SpliceTrap 0.90.5 [163] Biology, NGS, RNA-Seq
SPM 8 [164] Biology, Statistics, Neurology, Imaging
Sputnik 1.0 [165] Biology, Genomics
SRA 2.1.10 [166]] biology, NGS
SSPACE 2.0 [167] Biology, NGS
Stacks 0.9995 [168] Biology, Genomics, NGS
Structure 2.3.3 [169] Biology, Population
Swig 2.0.9 [170] Programming, C, C++, Python
TAU 2.21.4 [171] Profiling, Tracing, Programming
tgicl 2.1 [172] Biology, sequencing, clustering
Tophat 1.4.1, 2.0.1 [173] Biology, NGS
TreeFix 1.1.7 [174] Biology, Phylogenetics
TRF 4.04 [175] Biology, Genomics
Trimmomatic 0.22 [176] Biology, NGS
Trinity r20120905, r20121005, r20120225 [177] Biology, RNA-Seq
Twinscan 4.1.2 [178] Biology, Genomics
usearch 5.2.32 [179] Biology, Sequence analysis
VASP 4.6.34, 5.2.12, 5.3.2 [180] Quantum Chemistry, Ab Initio
VCFtools 0.1.9, 0.1.10 [181] Biology, SNPs
velvet 1.2.06, 1.2.07 [182] Biology, NGS
vmd 1.9.1 [183] Biology, Visualization
WebLogo 3.3 [184] Biology, Genomics
WDSSII 1 [185] Meteorology
WIEN2k 12.1 [186] Material Science, Chemistry
wgs 7.0.1.22 [187] Biology, NGS
wublast 2.0 [188] Biology, Sequence Alignment
Yasra 2.32 [189] 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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