Difference between revisions of "Installed Software"

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| [[ALLPATHS-LG]] || 42316, 44837 || [http://www.broadinstitute.org/software/allpaths-lg/blog/] || Biology, NGS
 
| [[ALLPATHS-LG]] || 42316, 44837 || [http://www.broadinstitute.org/software/allpaths-lg/blog/] || Biology, NGS
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|-
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| [[AFNI]] || 2011_12_21_1014 || [http://afni.nimh.nih.gov/afni] || Biology, Statistics, Imaging, Neurology
 
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| [[Amber]] || 11, 12 || [http://ambermd.org/] || Simulation, chemistry
 
| [[Amber]] || 11, 12 || [http://ambermd.org/] || Simulation, chemistry
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| [[SpliceTrap]] || 0.90.5 || [http://rulai.cshl.edu/splicetrap/] || Biology, NGS, RNA-Seq
 
| [[SpliceTrap]] || 0.90.5 || [http://rulai.cshl.edu/splicetrap/] || Biology, NGS, RNA-Seq
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| [[SPM]] || 8 || [http://www.fil.ion.ucl.ac.uk/spm/] || Biology, Statistics, Neurology, Imaging
 
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| [[Sputnik]] || 1.0 || [http://espressosoftware.com/sputnik/] || Biology, Genomics
 
| [[Sputnik]] || 1.0 || [http://espressosoftware.com/sputnik/] || Biology, Genomics

Revision as of 22:21, 24 April 2013

Installed Software List

Last updated 2013-04-24.

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
CellProfiler 2.0 [30] Biology, Image Analysis
Charmm 36a3 [31] Simulation, Chemistry
Circos 0.63-pre11 [32] Biology, Visualization
CisGenome 2.0 [33] Biology, Genomics, Peak Calling
ClustalW 2.1 [34] Biology, Genomics
CMake 2.8.8 [35] Programming
Consed 23.0 [36] Biology, Genomics
CUDA 4.2 [37] Programming, Graphics
Cufflinks 1.3.0, 2.0.0, 2.0.2 [38] Biology, NGS
Cutadapt 1.1 [39] Biology, NGS
Desmond 3.0.3.1 [40] Simulation, Biology, Chemistry
Dindel 1.01 [41] Biology, NGS
DIYABC many [42] Biology, Genomics
Dlpoly 4.03.4 [43] Simulation, Biology, Chemistry
Dock 6.5, 6.6 [44] Chemistry, ligand binding prediction
DTI-TK 2.3.1 [45] Bioinformatics, Neurology, Imaging
emboss 6.5.7 [46] Biology, multi-tool suite
Espresso 5.0.1 [47] Modeling, Physics
ESPRIT 201211 [48] Biology, NGS, Metagenomics
ETE2 2.1 [49] Biology, Phylogenetics
Eval 2.2.8 [50] Biology, Genomics, GUI
ExaML 20130314 [51] Biology, Phylogenetics
Exonerate 2.2.0 [52] Biology, Genomics
FAR 2.15 [53] Biology, Genomics
FASTA 34.26.5 [54] Biology, Genomics
FastQC 0.9.6, 0.10.1 [55] Biology, NGS
Fastx_toolkit 0.0.13.2 [56] Biology, NGS
Ferret 6.82 [57] Oceanography, Meteorology
FFTW 3.3.2 [58] Math, Library, C++
FragGeneScan 1.16 [59] Biology, NGS, Genomics
FreeBayes 0.9.6 [60] Biology
FSL 5.0.2.2 [61] Biology, Neurology, Imaging
Garli 2.0 [62] Biology, Phylogenetics
GATK 1.6.9 [63] Biology, NGS
Gaussian E01, G03, G09-A.02, G09-C.01 [64] Modeling, Computational Chemistry
GeneMark 2012.04 [65] Biology, Genomics, Metagenomics
Genewise 2.2.0 [66] Biology, Genomics, Annotation
GenomicTools 2.7.0 [67] Biology, NGS
Gmap 20070928, 20120712 [68] Biology, Genomics
GnuPlot 4.6.0 [69] Graphics, Plotting, Programming
Grace 5.1.22 [70] Graphics, plotting, 2D
GrADS 2.0.1 [71] Earth Science
Gromacs 4.5.5 [72] Chemistry, Modeling, Simulation
GSL 1.15 [73] Library, Math, C++, C
HaMStR v8b [74] Biology, Genomics
HDF5 1.8.9 [75] Library, Data
HMMER3 3.0 [76] Biology, Genomics
HTSeq 0.5.3p3 [77] Biology, NGS
HyPhy 2.1.2.28 [78] Biology, Phylogenetics
Hypre 2.8.0b [79] Library, Math, Physics
IDBA-UD 1.0.9, 1.1.0 [80] Biology, NGS
IM and IMa 20091217 [81] Biology, Population
IMa2 20120827 [82] Biology, Population
Intel Compilers 11.1, 2012 [83] Programming, Compilers
Iprscan 4.8 [84] Biology, Genomics
ITK 4.3.1 [85] Biology, Genomics
JDK 1.6.0_31, 1.7.0_02 [86] Java Development Kit
Kent 20120524 [87] Biology, NGS
Kmer 1934 [88] Biology, NGS
LAMMPS 28Oct12 [89] Molecular Dynamics Simulation
Last 193, 247 [90] Biology, Sequence alignment
Lastz 1.03.02, 1.02.00 [91] Biology, NGS
LIBSVM 3.12 [92] Machine Learning
MACS 1.4.2 [93] Biology, ChIP-Seq
mafft 6.903 [94] Biology, Multiple sequence alignment
Maker 2.10, 2.25b [95] Biology, Annotation, Genomics
Maq 0.7.1 [96] Biology, NGS
Matlab 2012a [97] Math, Simulation, Programming
MATS 2.1.0, 3.0.4, 3.0.6 [98] BIology, NGS
MCNP 5, 6b2 [99] Physics
MCNPX 2.7.0, 2.7.0-i8 [100] Physics
Meme 4.8.1 [101] Biology, Motifs, Sequence analysis
MetaCluster 5.0beta [102] Biology
MetaVelvet 1.2.01 [103] Biology, NGS
MetaGeneMark 2012.04 [104] Biology, Genomics
Midnight Commander 4.6.1 [105] Tools, Utilities
Migrate-n 3.3.0 [106] Biology, Population
mira 3.2.0, 3.4.0.1 [107] Biology, NGS
MISO 0.4.4 [108] Biology, NGS
MSMBuilder 2.5.1 [109] Molecular Dynamics
Molden 5.0 [110] Molecular, electronic structure
mosaik 2.1.33 [111] Biology,NGS
MrBayes 3.2.1 [112] Biology, Phylogenetics
MUMmer 3.23 [113] Biology, Genomics
MUSCLE 3.8.31 [114] Biology, Genomics
NAMD 2.9 [115] Simulation, Chemistry, Biology
Nbody 6 [116] Astronomy
NCO 4.2.1 [117] Data exchange tools
NetCDF 4.2 [118] Data exchange, Tools
Newbler 2.6, 2.7 [119] Biology, NGS
Novoalign 2.08.02, 3.00.02 [120] Biology, NGS
Oases 0.2.08 [121] Biology, NGS
Octave 3.6.4 [122] Numerical Computation
OpenFOAM 2.1.1 [123] Fluid Dynamics
OrthoMCL 2.0.2, 2.0.3, 2.0.7 [124] Biology, Genomics
PartitionFinder 1.0.1 [125] Biology, Phylogenetics, Evolution
Parflow v615 [126] Ecology, Modeling
PASA 1.5, r20120625 [127] Biology, Genomics
PeakSplitter 1.0 [128] Biology, Chip-Seq
PDT 3.18 [129] Programming, Profiler
Perl 5.16.0 [130] Programming, Language
PerM 0.4.0 [131] Biology, NGS
Phenix 1.8.1069 [132] Crystallography
PhyloBayes 3.3f [133] Biology, Phylogenetics
PhyML 3.0, 20121109 [134] Biology, Phylogenetics
Picard 1.69, 1.72, 1.80 [135] Biology, NGS
Proteinortho 4.26 [136] Biology, Genomics
python 2.6.8, 2.7.3 [137] Programming, scripting, language
QIIME 1.5.0 [138] Biology, Ecology
R 2.15.1, 2.15.0-mpi, Rmpi/2.15.1, 3.0.0 [139] Statistics, Programming
R8S 1.71 [140] Biology, Evolution
RADICAL 0.2 [141] Biology, Phylogenetics, Genomics
RAxML 7.3.2.0705 [142] Biology, Phylogenetics
RepeatMasker 3.3.0 [143] Biology, Genomics
Reptile 1.1 [144] Biology, NGS, error correction
riboPicker 0.4.3 [145] Biology, Sequence
RSEG 0.4.8 [146] Biology, NGS
samtools 0.1.16, 0.1.18, 0.1.19 [147] Biology, NGS
SAS 9.3 [148] Statistics, Graphing
SATe 2.2.7 [149] Biology, Phylogenetics
Schrodinger 2012 [150] Simulation, chemistry
SeqPrep 0.5 [151] Biology, NGS
SEQuel 1.0.1 [152] Biology, NGS
Sickle 1.200 [153] Biology, NGS, quality filter
Siesta 2.0.2,3.1 [154] Simulation, Physics, Ab Initio
SIFT 4.0.3b [155] Biology, Genomics
Silo 4.7 [156] Library, Data
Snap 20100728 [157] Biology, Genomics
SOAPdenovo 1.05 [158] Biology, NGS
SOAPdenovo-Trans 1.01 [159] Biology, NGS
SPARTA+ 2.60 [160] Chemistry
SPIMAP 1.1 [161] Biology, Phylogenetics
SpliceTrap 0.90.5 [162] Biology, NGS, RNA-Seq
SPM 8 [163] Biology, Statistics, Neurology, Imaging
Sputnik 1.0 [164] Biology, Genomics
SRA 2.1.10 [165]] biology, NGS
SSPACE 2.0 [166] Biology, NGS
Stacks 0.9995 [167] Biology, Genomics, NGS
Structure 2.3.3 [168] Biology, Population
Swig 2.0.9 [169] Programming, C, C++, Python
TAU 2.21.4 [170] Profiling, Tracing, Programming
tgicl 2.1 [171] Biology, sequencing, clustering
Tophat 1.4.1, 2.0.1 [172] Biology, NGS
TreeFix 1.1.7 [173] Biology, Phylogenetics
TRF 4.04 [174] Biology, Genomics
Trimmomatic 0.22 [175] Biology, NGS
Trinity r20120905, r20121005, r20120225 [176] Biology, RNA-Seq
Twinscan 4.1.2 [177] Biology, Genomics
usearch 5.2.32 [178] Biology, Sequence analysis
VASP 4.6.34, 5.2.12, 5.3.2 [179] Quantum Chemistry, Ab Initio
VCFtools 0.1.9, 0.1.10 [180] Biology, SNPs
velvet 1.2.06, 1.2.07 [181] Biology, NGS
vmd 1.9.1 [182] Biology, Visualization
WebLogo 3.3 [183] Biology, Genomics
WDSSII 1 [184] Meteorology
WIEN2k 12.1 [185] Material Science, Chemistry
wgs 7.0.1.22 [186] Biology, NGS
wublast 2.0 [187] Biology, Sequence Alignment
Yasra 2.32 [188] 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=11156"