Software-old: Difference between revisions

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| [[SOAPdenovo]] || 1.05 || Bioinformatics || zcluster ||  ||  
| [[SOAPdenovo]] || 1.05 || Bioinformatics || zcluster ||  ||  
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| [[SOAPdenovo-trans]] || 1.01 || Bioinformatics || zcluster || ||  
| [[SOAPdenovo-trans]] || 1.01 || Bioinformatics || zcluster || working, JKP ||  
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| [[SOAPdenovo2]] || r223 || Bioinformatics || zcluster || Working, JKP  ||  
| [[SOAPdenovo2]] || r223 || Bioinformatics || zcluster || JKP  ||  
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| [[SomaticCall]] || 42811 || Bioinformatics || zcluster || JKP ||  
| [[SomaticCall]] || 42811 || Bioinformatics || zcluster || JKP ||  

Revision as of 16:14, 6 February 2013

Installed Software List

Last updated 2013-02-06.

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

Software Template

Name Version Category Cluster Notes Reviewed By
00-Skipped Page 0.0 Work Log GACRC YH Created
3D_DOCK 2.0 Chemistry pcluster Ignored by SMW, YH reviewed, need SHT review
454 Software Bioinformatics zcluster Done, SMW
aaarf 1.0.0 Bioinformatics zcluster Done, SMW clear, YH
ABINIT 6.12.1 Chemistry zcluster Done, SMW
ABySS 1.3.4 Bioinformatics zcluster Done, SMW clear, YH
ALLPATHS-LG 44254 Bioinformatics zcluster Contains Dead Links, SMW
AMBER 11, 12 Chemistry zcluster Done, SHT
AMBER-pcluster 8 Chemistry pcluster
amos 3.1.0 Bioinformatics zcluster Done, SMW
Arabidopsis Database zcluster
ARB 5.3 Bioinformatics zcluster ?, Please Review Running Program Section, SMW clear, YH
Arb Database zcluster
AUGUSTUS 2.5.5 Bioinformatics zcluster Please verify Documentation Section, SMW
Bacteria NCBI Database zcluster
bam2fastq 1.1.0 Bioinformatics zcluster Done, SMW
BEAST 1.7.2 Bioinformatics zcluster Done, with Dead Links, SMW
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, YH
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, YH
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 working, JKP
SOAPdenovo2 r223 Bioinformatics zcluster JKP
SomaticCall 42811 Bioinformatics zcluster JKP
spimap 1.1 Bioinformatics zcluster JKP
SpliceGrapher 0.2.0 Bioinformatics zcluster JKP
SSAHA2 2.5.5 Bioinformatics zcluster JKP
SSPACE 2.0 Bioinformatics zcluster JKP
stacks 0.9993, 0.9996 Bioinformatics
STEM 2.0 Bioinformatics zcluster JKP
strauto 0.3.1 Bioinformatics zcluster JKP
structure 2.3.3 Bioinformatics zcluster JKP
Sus_scrofa Database zcluster
SVDetect r0.7m Bioinformatics zcluster JKP ?
SWIG 2.0.5 Utilities zcluster
T-Coffee 9.03.r1318 Bioinformatics zcluster JKP
tabix 0.2.5 Bioinformatics zcluster JKP
tagdust 1.12 Bioinformatics zcluster JKP ?
tassel 4.0 Bioinformatics zcluster JKP
tgicl 2.1 Bioinformatics zcluster JKP
TIGER 1.02 Bioinformatics zcluster JKP
tophat 2.0.5 Bioinformatics zcluster JKP
Tracer v 1.5 Bioinformatics zcluster JKP
Trinity r2012-10-05 Bioinformatics zcluster JKP
UNAFold 3.8 Bioinformatics zcluster JKP ?
Uniprot Database zcluster
Uniref Database zcluster
usearch v6.0.30 Bioinformatics zcluster JKP
vcftools 0.1.10 Bioinformatics zcluster Done, JKP; clear, YH
velvet 1.2.01 Bioinformatics zcluster JKP
VelvetOptimiser 2.2.4 Bioinformatics zcluster JKP
ViennaRNA 1.8.5 Bioinformatics zcluster JKP
vmatch 2.1.6 Bioinformatics zcluster JKP
VMD 1.9.1 Chemistry zcluster
wigToBigWig v 4 Bioinformatics zcluster JKP
WISE2 2.2.0 Bioinformatics zcluster JKP
WU Blast 2.2.6 Bioinformatics zcluster JKP
yasra 2.3 Bioinformatics zcluster JKP
Zz-example 0.0 Bioinformatics zcluster example for bioinformatics YH
Zz-template 0.0 Bioinformatics zcluster Template for bioinformatics YH
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