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| [[WU Blast]] || 2.2.6 || Bioinformatics || zcluster || | | [[WU Blast]] || 2.2.6 || Bioinformatics || zcluster || | ||
|- | |- | ||
| [[yasra]] || 2.3 || Bioinformatics || zcluster || | | [[yasra]] || 2.3 || Bioinformatics || zcluster || working, JP | ||
|- | |- | ||
| [[Zz-example]] || 0.0 || Bioinformatics || zcluster || example for bioinformatics YH | | [[Zz-example]] || 0.0 || Bioinformatics || zcluster || example for bioinformatics YH |
Revision as of 15:09, 5 February 2013
Installed Software List
Last updated 2013-02-05.
Note: Click on the icons to the right of the column headings to sort the table.
Name | Version | Category | Cluster | Notes |
---|---|---|---|---|
3D_DOCK | 2.0 | Chemistry | pcluster | SMW |
454 Software | Bioinformatics | zcluster | SMW | |
aaarf | 1.0.0 | Bioinformatics | zcluster | SMW |
ABINIT | 6.12.1 | Chemistry | zcluster | SMW |
ABySS | 1.3.4 | Bioinformatics | zcluster | |
ALLPATHS-LG | 44254 | Bioinformatics | zcluster | |
AMBER | 11, 12 | Chemistry | zcluster | Done, SHT |
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 | |
ESTscan | 3.0.3 | Bioinformatics | zcluster | Done, YH |
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 | Graphics | zcluster | Done, SHT |
gpu-blast | 1.1 with ncbi-blast-2.2.25+ | Bioinformatics | zcluster | |
grace | 5.1.22 | Other | zcluster | |
Gromacs | 4.5.5 | Chemistry | zcluster | Done, SHT |
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 | Done, Yecheng |
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 | Done, SHT |
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 | Working, Yecheng |
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 | working, JP |
Zz-example | 0.0 | Bioinformatics | zcluster | example for bioinformatics YH |
Zz-template | 0.0 | Bioinformatics | zcluster | Template for bioinformatics YH |