Difference between revisions of "Installed Software"

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[[Category:Software]]
 
[[Category:Software]]
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==Cluster Software Upgrade (Update 09/07/12)==
 
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The transition from RHEL5/CentOS5 to RHEL6 is, for all practical purposes, complete.  The "rhel5" queue has been stopped and is no longer accepting jobs and will be removed once the few remaining jobs complete.  The interactive nodes test01, test04, and test05 will be upgraded by the end of the day on Friday, September 7 (today).
 
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A majority of applications have been recompiled or otherwise re-installed under RHEL6.  There are still a few lightly used applications remaining that we should be able to finish next week.  If the software you need is not available and you have not already submitted a support request to have it installed, you may do so at http://support.hpc.ufl.edu.
 
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==Installed Software List==
 
==Installed Software List==
 
Last updated '''{{REVISIONYEAR}}-{{REVISIONMONTH}}-{{REVISIONDAY2}}'''.
 
Last updated '''{{REVISIONYEAR}}-{{REVISIONMONTH}}-{{REVISIONDAY2}}'''.
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| [[PAL2NAL]] || 14 || [http://www.bork.embl.de/pal2nal/]|| Biology, Genomics
 
| [[PAL2NAL]] || 14 || [http://www.bork.embl.de/pal2nal/]|| Biology, Genomics
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| [[PAML]] || 4.4e || [http://abacus.gene.ucl.ac.uk/software/paml.html]||Biology, Phylogenetics
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| [[PAML]] || 4.7 || [http://abacus.gene.ucl.ac.uk/software/paml.html]||Biology, Phylogenetics
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| [[PartitionFinder]] || 1.0.1 || [http://www.robertlanfear.com/partitionfinder/] || Biology, Phylogenetics, Evolution
 
| [[PartitionFinder]] || 1.0.1 || [http://www.robertlanfear.com/partitionfinder/] || Biology, Phylogenetics, Evolution

Revision as of 21:15, 18 June 2013

Installed Software List

Last updated 2013-06-18.

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
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, 2.2.27, 2.2.28 [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
Clview 20130402 [36] Biology, Genomics
CMake 2.8.8 [37] Programming
Consed 23.0 [38] Biology, Genomics
CUDA 4.2 [39] Programming, Graphics
Cufflinks 1.3.0, 2.0.0, 2.0.2 [40] Biology, NGS
Cutadapt 1.1 [41] Biology, NGS
Desmond 3.0.3.1 [42] Simulation, Biology, Chemistry
Dindel 1.01 [43] Biology, NGS
DIYABC many [44] Biology, Genomics
Dlpoly 4.03.4 [45] Simulation, Biology, Chemistry
Dock 6.5, 6.6 [46] Chemistry, ligand binding prediction
DTI-TK 2.3.1 [47] Bioinformatics, Neurology, Imaging
emboss 6.5.7 [48] Biology, multi-tool suite
Espresso 5.0.1 [49] Modeling, Physics
ESPRIT 201211 [50] Biology, NGS, Metagenomics
ETE2 2.1 [51] Biology, Phylogenetics
Eval 2.2.8 [52] Biology, Genomics, GUI
ExaML 20130314 [53] Biology, Phylogenetics
Exonerate 2.2.0 [54] Biology, Genomics
FAR 2.15 [55] Biology, Genomics
FASTA 34.26.5 [56] Biology, Genomics
FastQC 0.9.6, 0.10.1 [57] Biology, NGS
Fastx_toolkit 0.0.13.2 [58] Biology, NGS
Ferret 6.82 [59] Oceanography, Meteorology
FFTW 3.3.2 [60] Math, Library, C++
FragGeneScan 1.16 [61] Biology, NGS, Genomics
FreeBayes 0.9.6 [62] Biology
FSL 5.0.2.2 [63] Biology, Neurology, Imaging
Garli 2.0 [64] Biology, Phylogenetics
GATK 1.6.9 [65] Biology, NGS
Gaussian E01, G03, G09-A.02, G09-C.01 [66] Modeling, Computational Chemistry
GeneMark 2012.04 [67] Biology, Genomics, Metagenomics
Genewise 2.2.0 [68] Biology, Genomics, Annotation
GenomicTools 2.7.0 [69] Biology, NGS
Gmap 20070928, 20120712 [70] Biology, Genomics
GnuPlot 4.6.0 [71] Graphics, Plotting, Programming
Grace 5.1.22 [72] Graphics, plotting, 2D
GrADS 2.0.1 [73] Earth Science
Gromacs 4.5.5 [74] Chemistry, Modeling, Simulation
GSL 1.15 [75] Library, Math, C++, C
GULP 4.0 [76] Material Science
HaMStR v8b [77] Biology, Genomics
HDF5 1.8.9 [78] Library, Data
HMMER3 3.0 [79] Biology, Genomics
HOMER 4.2 [80] Biology, Genomics
HTSeq 0.5.3p3 [81] Biology, NGS
HyPhy 2.1.2.28 [82] Biology, Phylogenetics
Hypre 2.8.0b [83] Library, Math, Physics
IDBA-UD 1.0.9, 1.1.0 [84] Biology, NGS
IM and IMa 20091217 [85] Biology, Population
IMa2 20120827 [86] Biology, Population
Intel Compilers 11.1, 2012 [87] Programming, Compilers
Iprscan 4.8 [88] Biology, Genomics
ITK 4.3.1 [89] Biology, Genomics
Java 1.6.0_31, 1.7.0_02 [90] Java Development Kit
Kent 20120524 [91] Biology, NGS
Kmer 1934 [92] Biology, NGS
LAMMPS 28Oct12 [93] Molecular Dynamics Simulation
Last 193, 247 [94] Biology, Sequence alignment
Lastz 1.03.02, 1.02.00 [95] Biology, NGS
LIBSVM 3.12 [96] Machine Learning
MACS 1.4.2 [97] Biology, ChIP-Seq
mafft 7.037, 6.903 [98] Biology, Multiple sequence alignment
Maker 2.10, 2.25b [99] Biology, Annotation, Genomics
Maq 0.7.1 [100] Biology, NGS
Matlab 2012a [101] Math, Simulation, Programming
MATS 2.1.0, 3.0.4, 3.0.6 [102] BIology, NGS
Mauve 2.3.1 [103] Biology, Genomics, Multiple genome alignments
MCNP 5, 6b2 [104] Physics
MCNPX 2.7.0, 2.7.0-i8 [105] Physics
Meme 4.8.1 [106] Biology, Motifs, Sequence analysis
MetaCluster 5.0beta [107] Biology
MetaVelvet 1.2.01 [108] Biology, NGS
MetaGeneMark 2012.04 [109] Biology, Genomics
Midnight Commander 4.6.1 [110] Tools, Utilities
Migrate-n 3.3.0 [111] Biology, Population
mira 3.2.0, 3.4.0.1 [112] Biology, NGS
MISO 0.4.4 [113] Biology, NGS
MSMBuilder 2.5.1 [114] Molecular Dynamics
Molden 5.0 [115] Molecular, electronic structure
mosaik 2.1.33 [116] Biology,NGS
MrBayes 3.2.1 [117] Biology, Phylogenetics
MUMmer 3.23 [118] Biology, Genomics
MUSCLE 3.8.31 [119] Biology, Genomics
NAMD 2.9 [120] Simulation, Chemistry, Biology
Nbody 6 [121] Astronomy
NCO 4.2.1 [122] Data exchange tools
NetCDF 4.2 [123] Data exchange, Tools
Newbler 2.6, 2.7 [124] Biology, NGS
NMRPipe 7.9 [125] Biochemistry
Novoalign 2.08.02, 3.00.02 [126] Biology, NGS
Oases 0.2.08 [127] Biology, NGS
Octave 3.6.4 [128] Numerical Computation
OpenBabel 2.3.2 [129] Biology, Chemistry
OpenFOAM 2.1.1 [130] Fluid Dynamics
OrthoMCL 2.0.2, 2.0.3, 2.0.7 [131] Biology, Genomics
PAML 4.7 [132] Biology, Phylogenetics
PartitionFinder 1.0.1 [133] Biology, Phylogenetics, Evolution
Parflow v615 [134] Ecology, Modeling
PASA 1.5, r20120625 [135] Biology, Genomics
PeakSplitter 1.0 [136] Biology, Chip-Seq
PDT 3.18 [137] Programming, Profiler
Perl 5.16.0 [138] Programming, Language
PerM 0.4.0 [139] Biology, NGS
PETSc 2.3, 3.3 [140] Math, Numerical solvers
Phenix 1.8.1069 [141] Crystallography
PhyloBayes 3.3f [142] Biology, Phylogenetics
PhyML 3.0, 20121109 [143] Biology, Phylogenetics
Picard 1.69, 1.72, 1.80 [144] Biology, NGS
Proteinortho 4.26 [145] Biology, Genomics
python 2.6.8, 2.7.3 [146] Programming, scripting, language
QIIME 1.5.0 [147] Biology, Ecology
R 2.15.1, 2.15.0-mpi, Rmpi/2.15.1, 3.0.0 [148] Statistics, Programming
R8S 1.71 [149] Biology, Evolution
RADICAL 0.2 [150] Biology, Phylogenetics, Genomics
RAxML 7.3.2.0705 [151] Biology, Phylogenetics
RepeatMasker 3.3.0 [152] Biology, Genomics
Reptile 1.1 [153] Biology, NGS, error correction
riboPicker 0.4.3 [154] Biology, Sequence
RSEG 0.4.8 [155] Biology, NGS
samtools 0.1.16, 0.1.18, 0.1.19 [156] Biology, NGS
SAS 9.3 [157] Statistics, Graphing
SATe 2.2.7 [158] Biology, Phylogenetics
Schrodinger 2012 [159] Simulation, chemistry
SeqPrep 0.5 [160] Biology, NGS
SEQuel 1.0.1 [161] Biology, NGS
Sickle 1.200 [162] Biology, NGS, quality filter
Siesta 2.0.2,3.1 [163] Simulation, Physics, Ab Initio
SIFT 4.0.3b [164] Biology, Genomics
Silo 4.7 [165] Library, Data
Snap 20100728 [166] Biology, Genomics
SOAPdenovo 1.05 [167] Biology, NGS
SOAPdenovo-Trans 1.01 [168] Biology, NGS
SPARTA+ 2.60 [169] Chemistry
SPIMAP 1.1 [170] Biology, Phylogenetics
SpliceTrap 0.90.5 [171] Biology, NGS, RNA-Seq
SPM 8 [172] Biology, Statistics, Neurology, Imaging
Sputnik 1.0 [173] Biology, Genomics
SRA 2.1.10 [174]] biology, NGS
SSPACE 2.0 [175] Biology, NGS
Stacks 0.9995 [176] Biology, Genomics, NGS
Structure 2.3.3 [177] Biology, Population
SUNDIALS 2.5.0 [178] Numerical Solver
swak4Foam 2.x [179] Fluid Dynamics
Swig 2.0.9 [180] Programming, C, C++, Python
TAU 2.21.4 [181] Profiling, Tracing, Programming
tgicl 2.1 [182] Biology, sequencing, clustering
Tophat 1.4.1, 2.0.1, 2.0.8b [183] Biology, NGS
TreeFix 1.1.7 [184] Biology, Phylogenetics
TRF 4.04 [185] Biology, Genomics
Trimmomatic 0.22 [186] Biology, NGS
Trinity r20120905, r20121005, r20120225 [187] Biology, RNA-Seq
Twinscan 4.1.2 [188] Biology, Genomics
usearch 5.2.32 [189] Biology, Sequence analysis
VASP 4.6.34, 5.2.12, 5.3.2 [190] Quantum Chemistry, Ab Initio
VCFtools 0.1.9, 0.1.10 [191] Biology, SNPs
velvet 1.2.06, 1.2.07 [192] Biology, NGS
vmd 1.9.1 [193] Biology, Visualization
WebLogo 3.3 [194] Biology, Genomics
WDSSII 1 [195] Meteorology
WIEN2k 12.1 [196] Material Science, Chemistry
wgs 7.0.1.22 [197] Biology, NGS
wublast 2.0 [198] Biology, Sequence Alignment
Yambo 3.3.0 [199] Physics
Yasra 2.32 [200] 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=11344"