Software-old

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Revision as of 11:48, 1 February 2013 by Yhuang (talk | contribs)
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Installed Software List

Last updated 2013-02-01.

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

Software Template

Name Version Category Cluster Notes
3D_DOCK 2.0 Chemistry pcluster
454 Software zcluster
aaarf 1.0.0 Bioinformatics zcluster
ABINIT 6.12.1 Chemistry zcluster
ABySS 1.3.4 Bioinformatics zcluster
ALLPATHS-LG 44254 Bioinformatics zcluster
AMBER 11, 12 Chemistry zcluster
AMBER-pcluster 8 Chemistry pcluster
amos 3.1.0 Bioinformatics zcluster
Arabidopsis Database zcluster
ARB 5.3 Bioinformatics zcluster
Arb Database zcluster
AUGUSTUS 2.5.5 Bioinformatics zcluster
Bacteria NCBI Database zcluster
bam2fastq 1.1.0 Bioinformatics zcluster
BEAST 1.7.2 Bioinformatics zcluster
BEDTools 2.16.2 Bioinformatics zcluster
BEST Bayesian 2.3.1 Bioinformatics zcluster
BioPerl 1.61 Bioinformatics zcluster
BioPython 1.58 Bioinformatics zcluster
Bismark Bisulfite Mapper 0.7.6 Bioinformatics zcluster
BiSS 0.0.1 Bioinformatics zcluster
Bl2seq Bioinformatics zcluster
BLAST Databases Database zcluster
Blastall Bioinformatics zcluster
BLASTCLUST Bioinformatics zcluster
Blastpgp Bioinformatics zcluster
Blat 3.5 Bioinformatics zcluster
BMGE 1.1 Bioinformatics zcluster
bowtie 0.12.8 Bioinformatics zcluster
bowtie2 2.0.0-beta7 Bioinformatics zcluster
breakdancer 1.1_2011_02_21 Bioinformatics zcluster
brownie 2.1.2 Bioinformatics zcluster
BS Seeker Dec 113 Bioinformatics zcluster
Burrows-Wheeler Aligner (BWA) 0.6.2 Bioinformatics zcluster
cd-hit 4.5.6 Bioinformatics zcluster
cdbfasta 04282012 Bioinformatics zcluster
CEAS 1.0.2 Bioinformatics zcluster
CEGMA 2.4.010312 Bioinformatics zcluster
circos 0.62 Bioinformatics zcluster
ClustalW 2.1 Bioinformatics zcluster
Coding Potential Calculator 0.9-r2 Bioinformatics zcluster
COG zcluster
CONSEL v0.20 Bioinformatics zcluster
cortex_con 0.04c Bioinformatics zcluster
cortex_var 1.0.5.3 Bioinformatics zcluster
Count 2010-04-02 Bioinformatics zcluster
CREST 1.0 Bioinformatics zcluster
ctrax 0.3.2 Other zcluster
cufflinks 2.0.2 Bioinformatics zcluster
cutadapt 1.1 Bioinformatics zcluster
ddRADseq Bioinformatics zcluster
DLCoal 1.0 Bioinformatics zcluster
drmma 0.5 Other zcluster
ea-utils 1.1.2-537 Bioinformatics zcluster
edena 3Dev120626 Bioinformatics zcluster
EMBOSS 6.2.0 Bioinformatics zcluster
emmix 1.3 Bioinformatics zcluster
evm (EVidenceModeler) r2012-06-25 Bioinformatics zcluster
ExaML 315576 Bioinformatics zcluster
exonerate 2.2.0 Bioinformatics zcluster
FAR 2.15 Bioinformatics zcluster
FASTA 36 Bioinformatics zcluster
FastQC 0.10.1 Bioinformatics zcluster
fasttree 2.1.4 Bioinformatics zcluster
FastX 0.0.13, 0.0.13.2 Bioinformatics zcluster
FIRE 1.1 Bioinformatics zcluster
FISH Database zcluster
FitModel 0.5.3 Bioinformatics zcluster
FLASH 1.0.3 Bioinformatics zcluster
GAMESS May2012R1 with XMVB 2.0. Chemistry zcluster
GAMESS-pcluster 2007 R6 Chemistry pcluster
GapFiller 1.11 Bioinformatics zcluster
gatk 2.2-2-gf44cc4e Bioinformatics zcluster
GAUSSIAN03 03 Chemistry pcluster
GAUSSIAN94 94 Chemistry pcluster
Gblocks 0.91b Bioinformatics zcluster
GeneMark genemark-ES 2.3e gGeneMark version 2.5m Bioinformatics zcluster
Genome Phred version: 0.071220.c Bioinformatics zcluster
GenomeMapper 0.4.3 (Version for SHORE/WMD3) Bioinformatics zcluster
GenomeTools 1.3.9 Bioinformatics zcluster
git 1.7.4.1, 1.7.9 Others zcluster
Glimmer 3.0.2 Bioinformatics zcluster
GlimmerHMM 3.0.1 Bioinformatics zcluster
gmap 2007-09-28 Bioinformatics zcluster
gmap-gsnap 2012-07-20 Bioinformatics zcluster
gnuplot 4.0, 4.6.0 Other zcluster
gpu-blast 1.1 with ncbi-blast-2.2.25+ Bioinformatics zcluster
grace 5.1.22 Other zcluster
Gromacs 4.5.5 Chemistry zcluster
gss Bioinformatics zcluster
HDF5 1.6.4, 1.8.9 Other zcluster
Hmmer 3.0 Bioinformatics zcluster
Homo_sapien Database zcluster
htgs Database zcluster
htseq 0.5.3p3 Bioinformatics zcluster
igb 6.7.3 Bioinformatics zcluster
IGV 2.1.23 Bioinformatics zcluster
IMa May 06 Bioinformatics zcluster
indel-Seq-Gen 2.02 Bioinformatics zcluster
InStruct 3.2.09 Bioinformatics zcluster
iprscan (InterProScan) 5.0 CR2 Bioinformatics zcluster
iscan 1.0.0 Bioinformatics zcluster
Jellyfish 1.1.5 Bioinformatics zcluster
k-link 03 27, 2009 Bioinformatics zcluster
KEGG Database zcluster
LASTZ 1.03.02 Bioinformatics zcluster
LDDist 1.3.2 Bioinformatics zcluster
libsequence 1.7.4 Bioinformatics zcluster
LLVM-Clang 3.1 Compiler zcluster
lsa 11182011 Bioinformatics zcluster
macs 1.4.2 Bioinformatics zcluster
mafft 6.864b Bioinformatics zcluster
maize Database zcluster
maker 2.10 Bioinformatics zcluster
Maple-pcluster 10.06 Other pcluster
MAQ 0.7.1 Bioinformatics zcluster
Mathematica 5.2 Other pcluster
MatLab R2012a (7.14.0.739) Other zcluster
MCL 12-135 Bioinformatics zcluster
MEAD 2.2.9 Chemistry zcluster
Medicago Database zcluster
megan 4.67.2 Bioinformatics zcluster
MEME 4.8.1 Bioinformatics zcluster
Migrate 3.0.3 Bioinformatics zcluster
Minia 1.4683 Bioinformatics zcluster
MIRA 3.9.9 Bioinformatics zcluster
MOTECC qmdcp 90 Chemistry zcluster
MOTECC qmdcp pcluster 90 Chemistry pcluster
MOTHUR 1.28.0 Bioinformatics zcluster
mpi4py 1.3 Utilities zcluster
mpiblast 1.6.0 Bioinformatics zcluster
MrBayes 3.1.2 Bioinformatics zcluster
mrfast 2.5.0.4 Bioinformatics zcluster
MSA 3.8.1b Bioinformatics zcluster
MUSCLE 3.8.31 Bioinformatics zcluster
MyScanACE 04232012 Bioinformatics zcluster
NAMD 2.9 Chemistry zcluster
NAMD-pcluster 2.6b2, 2.7b1 Chemistry pcluster
NCBI Blast 2.2.26 Bioinformatics zcluster Yecheng Done
NCBI Blast + 2.2.26 Bioinformatics zcluster
ncbi blast parsers Bioinformatics zcluster
NCBI_database Bioinformatics zcluster
NETCDF 4.1.3 Other zcluster
NETCDF-pcluster 3.5.1, 3.6.2 Other pcluster
netlogo 5.0 Other zcluster
Newbler 2.6 Bioinformatics zcluster
NH PhyloBayes 0.2.3 Bioinformatics zcluster
nhPhyML 01/2012 Bioinformatics zcluster
NovelSeq 1.0.2 Bioinformatics zcluster
NovoAlign 2.07 Bioinformatics zcluster
numexp 1.4.2 Other zcluster
NWCHEM 4.7 Chemistry pcluster
opal 2.0.0 Bioinformatics zcluster
Open Babel 2.3.1 Chemistry zcluster
OpenBUGS 3.2.2 Statistics zcluster
OpenCV 2.3.1 Other zcluster
OSPREY 2.0 Bioinformatics zcluster
p4 r231 Bioinformatics zcluster
pagan 0.39 Bioinformatics zcluster
PAML 4.4 Bioinformatics zcluster
pandaseq 2.0 Bioinformatics zcluster
Papara_nt 2.1.2 Bioinformatics zcluster
PASHA 1.0.6 Bioinformatics zcluster
PeakSplitter 1.0 Bioinformatics zcluster
pebl 1.01 zcluster
pfam 26.0 Database zcluster
Pfam_scan 04282012 Bioinformatics zcluster
pftools 2.3.5 Bioinformatics zcluster
phred/phrap/conced zcluster
PhyloBayes 3.3b Bioinformatics zcluster
PHYML 20110919 Bioinformatics zcluster
picard 1.62 Bioinformatics zcluster
Populus Database zcluster
prank 100802 Bioinformatics zcluster
Primer3 2.3.4 Bioinformatics zcluster
pysam 0.6 Bioinformatics zcluster
PyTables 2.3.1 Other zcluster
Qiime 1.6.0 Bioinformatics zcluster
QTL Cartographer 1.17j Bioinformatics zcluster
quake 0.3.4 Bioinformatics zcluster
Quantum Espresso 5.0.2 Chemistry zcluster
R 2.14.0, 2.15.0, 2.15.2 Statistics zcluster
R-pcluster 1.9.1, 2.1.1, 2.4.0 pcluster
RAxML 04/26/2012 Bioinformatics zcluster
RAxML-Light 1.0.5 Bioinformatics zcluster
Ray 1.6.1-0 Bioinformatics zcluster
RCCBatchBlast 5.0 Bioinformatics zcluster
RCCBatchBlastPlus 1.0 Bioinformatics zcluster Yecheng working
RECON 1.05 Bioinformatics zcluster
Refseq Database zcluster
Repeatmasker 3.3 Bioinformatics zcluster
RepeatScout 1.05 Bioinformatics zcluster
riboPicker 0.4.3 Bioinformatics zcluster
Rice TIGR Database zcluster
RMBlast 2.2.27 Bioinformatics zcluster
Rmpi 0.5-9 Statistics zcluster
RNAz 2.1 Bioinformatics zcluster
rnnotator 2.4.12 Bioinformatics zcluster
Roche 2.6 Bioinformatics zcluster
Roseobacter Database zcluster
RSAT 1.0 Bioinformatics zcluster
RSEM 1.1.21, 1.2.0 Bioinformatics zcluster
RTD git at 11/28/2012 Bioinformatics zcluster
RUM 1.11 Bioinformatics zcluster
Sage 3.1.1, 3.4.1 Other zcluster
samtools 0.1.18 Bioinformatics zcluster
SAS 9.1 Statistics zcluster
SATé 2.2.4 Bioinformatics zcluster
SEQuel 1.0.2 Bioinformatics zcluster
SHE-RA 012012 Bioinformatics zcluster
SHORE 0.8 Bioinformatics zcluster
sickle 1.200 Bioinformatics zcluster
Silva Database zcluster
SiZer 07022012 Bioinformatics zcluster
slclust 04282012 Bioinformatics zcluster
SNAP 2010-7-28 Bioinformatics zcluster
snow 0.3-8 Statistics zcluster
snowhite 1.1.4 Bioinformatics zcluster
snpEff 2_0_5d Bioinformatics zcluster
SOAPdenovo 1.05 Bioinformatics zcluster
SOAPdenovo-trans 1.01 Bioinformatics zcluster
SOAPdenovo2 r223 Bioinformatics zcluster
SomaticCall 42811 Bioinformatics zcluster
spimap 1.1 Bioinformatics zcluster
SpliceGrapher 0.2.0 Bioinformatics zcluster
SSPACE 2.0 Bioinformatics zcluster
stacks 0.9993, 0.9996 Bioinformatics
STEM 2.0 Bioinformatics zcluster
strauto 0.3.1 Bioinformatics zcluster
structure 2.3.3 Bioinformatics zcluster
Sus_scrofa Database zcluster
SVDetect r0.7m Bioinformatics zcluster
SWIG 2.0.5 Utilities zcluster
T-Coffee 9.03.r1318 Bioinformatics zcluster
tabix 0.2.5 Bioinformatics zcluster
tagdust 1.12 Bioinformatics zcluster
tassel 4.0 Bioinformatics zcluster
tgicl 2.1 Bioinformatics zcluster
TIGER 1.02 Bioinformatics zcluster
tophat 2.0.5 Bioinformatics zcluster
Tracer v 1.5 Bioinformatics zcluster
Trinity r2012-10-05 Bioinformatics zcluster
UNAFold 3.8 Bioinformatics zcluster
Uniprot Database zcluster
Uniref Database zcluster
usearch v6.0.30 Bioinformatics zcluster
vcftools 0.1.10 Bioinformatics zcluster
velvet 1.2.01 Bioinformatics zcluster
VelvetOptimiser 2.2.4 Bioinformatics zcluster
ViennaRNA 1.8.5 Bioinformatics zcluster
vmatch 2.1.6 Bioinformatics zcluster
VMD 1.9.1 Chemistry zcluster
wigToBigWig v 4 Bioinformatics zcluster
WISE2 2.2.0 Bioinformatics zcluster
WU Blast 2.2.6 Bioinformatics zcluster
yasra 2.3 Bioinformatics zcluster
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