Software-old

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Revision as of 00:05, 31 January 2013 by Yhuang (talk | contribs)
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Installed Software List

Last updated 2013-01-31.

Note: Click on the icons to the right of the column headings to sort the table.

Software Template

Name Version Category Website Cluster Notes
ARB 5.3 Bioinformatics zcluster
BEAST 1.7.2 Bioinformatics zcluster
BEST Bayesian 2.3.1 Bioinformatics
BioPerl 1.61 Bioinformatics zcluster
BioPython 1.58 Bioinformatics zcluster
NCBI Blast 2.2.26 is the last updated. older versions are also available. Bioinformatics zcluster
RCCBatchBlast 4.0 Bioinformatics zcluster
Blat 3.5 Bioinformatics zcluster
ClustalW 2.1 Bioinformatics zcluster
CONSEL v0.20 Bioinformatics zcluster
EMBOSS 6.2.0 (updated at 04/17/2010) Bioinformatics zcluster
FASTA 36 Bioinformatics zcluster
FIRE 1.1 Bioinformatics zcluster
FitModel 0.5.3 Bioinformatics zcluster
Genome Phred version: 0.071220.c
Hmmer 3.0 Bioinformatics
IMa May 06 Bioinformatics
indel-Seq-Gen 2.02 Bioinformatics
iprscan (InterProScan) 5.0 CR2 Bioinformatics
MEME 4.8.1 Bioinformatics zcluster
Migrate 3.0.3 Bioinformatics
MrBayes 3.1.2 Bioinformatics
MUSCLE 3.8.31 Bioinformatics zcluster
PAML Latest version 4.4 Bioinformatics zcluster
Pfam_scan 04282012 Bioinformatics zcluster
pftools 2.3.5 Bioinformatics zcluster
PHYML 20110919 Bioinformatics
RAxML 04/26/2012 Bioinformatics zcluster
Repeatmasker 3.3 Bioinformatics zcluster
RepeatScout 1.05 Bioinformatics zcluster
STEM 2.0 Bioinformatics zcluster
Tracer v 1.5 Bioinformatics zcluster
WISE2 2.2.0 Bioinformatics zcluster
3D_DOCK 2.0 Computational Chemistry pcluster
AMBER- 8 Computational Chemistry pcluster
GAMESS 2007 R6 pcluster
GAUSSIAN03 03 Computational Chemistry pcluster
GAUSSIAN94 94 Computational Chemistry pcluster
MOTECC qmdcp 90 Computational Chemistry pcluster
NWCHEM 4.7 Computational Chemistry pcluster
VMD 1.8.4 Computational Chemistry zcluster
Maple-pcluster 10.06 Other pcluster
Mathematica 5.2 Other pcluster
MatLab R2012a (7.14.0.739) Other zcluster
NETCDF 3.5.1, 3.6.2 Other pcluster
Sage 3.1.1, 3.4.1 Other
R 1.9.1, 2.1.1, 2.4.0 pcluster
R 2.4.0, 2.5.1, 2.7.0 zcluster
SAS 9.1 Statistics
Bl2seq Bioinformatics
Blastall Bioinformatics zcluster
BLASTCLUST Bioinformatics
BLAST Databases
Blastpgp Bioinformatics
fastacmd
Formatdb
MEGABLAST
Arabidopsis Database zcluster
Arb zcluster
Bacteria NCBI zcluster
COG zcluster
NCBI_database Bioinformatics zcluster
gss Bioinformatics zcluster
FISH zcluster
Homo_sapien zcluster
htgs zcluster
KEGG zcluster
Medicago zcluster
Populus zcluster
Refseq zcluster
Rice TIGR zcluster
Roseobacter zcluster
Silva zcluster
Sus_scrofa zcluster
Uniprot zcluster
Uniref zcluster
WU Blast 2.2.6 Bioinformatics zcluster
AMBER 8, 10 Computational Chemistry zcluster
NAMD 2.6b2, 2.7b1 Computational Chemistry pcluster
NovoAlign 2.07 Bioinformatics zcluster
MAQ 0.7.1 Bioinformatics zcluster
MIRA 3.9.9 Bioinformatics zcluster
pebl 1.01 installed for Python 2.6.2
Burrows-Wheeler Aligner (BWA) 0.6.2 zcluster
maize Database zcluster
RCAC Awards 1.3M+ CPU Hours
tophat 2.0.5 Bioinformatics zcluster
pfam 26.0 database zcluster
ncbi blast parsers Bioinformatics zcluster
Newbler 2.6 Bioinformatics zcluster
MOTHUR 1.8.0, 1.9.0, 1.12.0 zcluster
velvet 1.2.01 Bioinformatics zcluster
bowtie 0.12.8 Bioinformatics zcluster
Qiime 1.3.0 Bioinformatics zcluster
QTL Cartographer 1.17j Bioinformatics zcluster
ViennaRNA 1.8.5 Bioinformatics zcluster
RNAz 2.1 Bioinformatics zcluster
AUGUSTUS 2.5.5 Bioinformatics zcluster
GlimmerHMM 3.0.1 Bioinformatics zcluster
SNAP 2010-7-28 Bioinformatics zcluster
exonerate 2.2.0 Bioinformatics zcluster
GeneMark genemark-ES 2.3e gGeneMark version 2.5m Bioinformatics zcluster
UNAFold 3.8 Bioinformatics zcluster
maker 2.10 Bioinformatics zcluster
mpiblast 1.6.0 Bioinformatics zcluster
prank 100802 Bioinformatics zcluster
cufflinks 2.0.2 Bioinformatics zcluster
phred/phrap/conced
454 Software
Roche 2.6 Bioinformatics zcluster
SHE-RA 012012 Bioinformatics zcluster
NCBI Blast + 2.2.26 is the last updated Bioinformatics zcluster
LASTZ 1.03.02 Bioinformatics zcluster
samtools 0.1.18 Bioinformatics zcluster
git 1.7.4.1, 1.7.9 Others
BS Seeker download at Dec 113 Bioinformatics
mafft 6.864b Bioinformatics zcluster
opal 2.0.0 Bioinformatics zcluster
SATé 2.2.4 Bioinformatics zcluster
MOTECC qmdcp 90 Computational Chemistry zcluster
Ray 1.4.0, 1.6.1-0 Bioinformatics
Trinity Versions r2012-10-05 Bioinformatics zcluster
k-link 03 27, 2009 Bioinformatics
FastX Version 0.0.13, 0.0.13.2 Bioinformatics
MyScanACE 04232012 Bioinformatics zcluster
gatk 2.2-2-gf44cc4e Bioinformatics zcluster
breakdancer 1.1_2011_02_21 Bioinformatics zcluster
CREST 1.0 Bioinformatics zcluster
SOAPdenovo 1.05 Bioinformatics zcluster
SEQuel 1.0.2 Bioinformatics zcluster
cd-hit 4.5.6 Bioinformatics zcluster
amos 3.1.0 Bioinformatics zcluster
lsa 11182011 Bioinformatics zcluster
mrfast 2.5.0.4 Bioinformatics zcluster
tassel 4.0 Bioinformatics zcluster
TIGER 1.02 Bioinformatics zcluster
BMGE 1.1 Bioinformatics zcluster
nhPhyML downloaded at 01/2012 Bioinformatics zcluster
pagan 0.39 Bioinformatics zcluster
NH PhyloBayes 0.2.3 Bioinformatics zcluster
LDDist 1.3.2 Bioinformatics zcluster
strauto 0.3.1 Bioinformatics zcluster
PhyloBayes 3.3b Bioinformatics zcluster
SOAPdenovo-trans 1.01 Bioinformatics zcluster
gpu-blast 1.1 with ncbi-blast-2.2.25+ Bioinformatics zcluster
R 2.14.0, 2.15.0 Statistics
Gromacs 4.5.5 Computational Chemistry zcluster
picard 1.62 Bioinformatics zcluster
ALLPATHS-LG 44254 Bioinformatics zcluster
Quantum Espresso 4.3.2, 5.0.2 Computational Chemistry
ABINIT 6.12.1 Computational Chemistry zcluster
MOTHUR 1.28.0 Bioinformatics zcluster
snow 0.3-8 Statistics zcluster
Rmpi 0.5-9 Statistics zcluster
iscan 1.0.0 Bioinformatics zcluster
p4 r231 Bioinformatics zcluster
tgicl 2.1 Bioinformatics zcluster
NETCDF 4.1.3 Other zcluster
GenomeTools 1.3.9 Bioinformatics zcluster
snpEff 2_0_5d Bioinformatics zcluster
drmma 0.5 Others zcluster
aaarf 1.0.0 bioinformatics zcluster
netlogo 5.0 Other zcluster
ctrax 0.3.2 Other zcluster
pysam 0.6 Bioinformatics zcluster
OpenCV 2.3.1 Other zcluster
mpi4py 1.3 Utilities zcluster
grace 5.1.22 Others zcluster
gnuplot 4.0, 4.6.0 Other
SWIG 2.0.5 Utilities zcluster
megan 4.67.2 Bioinformatics zcluster
yasra 2.3 Bioinformatics zcluster
gmap 2007-09-28 Bioinformatics zcluster
cdbfasta 04282012 Bioinformatics zcluster
slclust 04282012 Bioinformatics zcluster
htseq 0.5.3p3 Bioinformatics zcluster
AMBER 11, 12 Computational Chemistry
OSPREY 2.0 Bioinformatics zcluster
vmatch 2.1.6 Bioinformatics zcluster
rnnotator 2.4.12 Bioinformatics zcluster
tagdust 1.12 Bioinformatics zcluster
snowhite 1.1.4 Bioinformatics zcluster
gmap-gsnap 2012-07-20 Bioinformatics zcluster
bowtie2 2.0.0-beta7 Bioinformatics zcluster
spimap 1.1 Bioinformatics zcluster
DLCoal 1.0 Bioinformatics zcluster
structure 2.3.3 Bioinformatics zcluster
vcftools 0.1.10 Bioinformatics zcluster
Coding Potential Calculator 0.9-r2 Bioinformatics zcluster
Qiime 1.6.0 Bioinformatics zcluster
HDF5 1.6.4, 1.8.9 Other
ABySS 1.3.4 Bioinformatics zcluster
RUM 1.11 Bioinformatics zcluster
Count 2010-04-02 Bioinformatics zcluster
cutadapt 1.1 Bioinformatics zcluster
MCL 12-135 Bioinformatics zcluster
T-Coffee 9.03.r1318 Bioinformatics zcluster
Primer3 2.3.4 Bioinformatics zcluster
tabix 0.2.5 Bioinformatics zcluster
numexp 1.4.2 Other zcluster
PyTables 2.3.1 Other zcluster
BEDTools 2.16.2 Bioinformatics zcluster
circos 0.62 Bioinformatics zcluster
SVDetect r0.7m Bioinformatics zcluster
cortex_con 0.04c Bioinformatics zcluster
stacks 0.9993, 0.9996 Bioinformatics
cortex_var 1.0.5.3 Bioinformatics zcluster
edena 3Dev120626 Bioinformatics zcluster
emmix 1.3 Bioinformatics zcluster
SiZer 07022012 Bioinformatics zcluster
macs 1.4.2 Bioinformatics zcluster
evm (EVidenceModeler) r2012-06-25 Bioinformatics zcluster
FLASH 1.0.3 Bioinformatics zcluster
pandaseq 2.0 Bioinformatics zcluster
fasttree 2.1.4 Bioinformatics zcluster
Papara_nt 2.1.2 Bioinformatics zcluster
Gblocks 0.91b Bioinformatics zcluster
NAMD 2.9 Computational Chemistry zcluster
FAR 2.15 Bioinformatics zcluster
FastQC 0.10.1 Bioinformatics zcluster
brownie 2.1.2 Bioinformatics zcluster
Bismark Bisulfite Mapper 0.7.6 Bioinformatics zcluster
Glimmer 3.0.2 Bioinformatics zcluster
bam2fastq 1.1.0 Bioinformatics zcluster
quake 0.3.4 Bioinformatics zcluster
Jellyfish 1.1.5 Bioinformatics zcluster
BiSS 0.0.1 Bioinformatics zcluster
SomaticCall 42811 Bioinformatics zcluster
IGV 2.1.23 Bioinformatics zcluster
igb 6.7.3 Bioinformatics zcluster
PeakSplitter 1.0 Bioinformatics zcluster
CEAS 1.0.2 Bioinformatics zcluster
OpenBUGS 3.2.2 Statistics zcluster
VelvetOptimiser 2.2.4 Bioinformatics zcluster
LLVM-Clang 3.1 Utilities zcluster
sickle 1.200 Bioinformatics zcluster
GenomeMapper 0.4.3 (Version for SHORE/WMD3) Bioinformatics zcluster
SHORE 0.8 Bioinformatics zcluster
PASHA 1.0.6 Bioinformatics zcluster
RAxML-Light 1.0.5 Bioinformatics zcluster
ExaML 315576 Bioinformatics zcluster
riboPicker 0.4.3 Bioinformatics zcluster
RMBlast 2.2.27 Bioinformatics zcluster
RSEM 1.1.21, 1.2.0 Bioinformatics
MEAD 2.2.9 Computational Chemistry zcluster
Open Babel 2.3.1 Computational Chemistry zcluster
SpliceGrapher 0.2.0 Bioinformatics zcluster
wigToBigWig v 4 Bioinformatics zcluster
MSA 3.8.1b Bioinformatics zcluster
libsequence 1.7.4 Bioinformatics zcluster
GAMESS May2012R1 with XMVB 2.0. Computational Chemistry
RECON 1.05 Bioinformatics zcluster
CEGMA 2.4.010312 Bioinformatics zcluster
SSPACE 2.0 Bioinformatics zcluster
RSAT 1.0 Bioinformatics zcluster
RTD git at 11/28/2012 Bioinformatics zcluster
ddRADseq Bioinformatics zcluster
usearch v6.0.30 Bioinformatics zcluster
GapFiller 1.11 Bioinformatics zcluster
InStruct 3.2.09 Bioinformatics zcluster
NovelSeq 1.0.2 Bioinformatics zcluster
SOAPdenovo2 r223 Bioinformatics zcluster
Minia 1.4683 Bioinformatics zcluster
ea-utils 1.1.2-537 Bioinformatics zcluster
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