Software-old

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Installed Software List

Last updated 2013-02-12.

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, clear, SHT
454 Software Bioinformatics zcluster Done, SMW clear, YH
aaarf 1.0.0 Bioinformatics zcluster Done, SMW clear, YH
ABINIT 6.12.1 Chemistry zcluster Done, SMW clear, SHT
ABySS 1.3.4 Bioinformatics zcluster Done, SMW clear, YH
ALLPATHS-LG 44254 Bioinformatics zcluster Contains Dead Links, SMW clear, YH
AMBER 11, 12 Chemistry zcluster Done, SHT clear, SHT
AMBER-pcluster 8 Chemistry pcluster
amos 3.1.0 Bioinformatics zcluster Done, SMW clear, YH
ARB 5.3 Bioinformatics zcluster ?, Please Review Running Program Section, SMW clear, YH
AUGUSTUS 2.5.5 Bioinformatics zcluster Please verify Documentation Section, SMW clear, YH
bam2fastq 1.1.0 Bioinformatics zcluster Done, SMW clear, YH
BEAST 1.7.2 Bioinformatics zcluster Done, with Dead Links, SMW clear, YH 2/7 8:30 am YH
BEDTools 2.16.2 Bioinformatics zcluster Done, SMW clear, YH
BEST Bayesian 2.3.1 Bioinformatics zcluster Done, SMW clear, YH
Bio++ 2.0.3 Bioinformatics zcluster working, SHT
BioPerl 1.61 Bioinformatics zcluster Done, SMW clear, YH
BioPython 1.58 Bioinformatics zcluster Done, SMW clear, YH
Bismark Bisulfite Mapper 0.7.6 Bioinformatics zcluster Done, SMW clear, YH
BiSS 0.0.1 Bioinformatics zcluster Done, SMW clear, YH
BLAS 3.0 Math Library zcluster Done, SHT clear, SHT
Blat 3.5 Bioinformatics zcluster Done, SMW clear, YH
BMGE 1.1 Bioinformatics zcluster Done, SMW clear, YH
Boost 1.47.0, 1.48.0 Library zcluster Done, SHT clear, SHT
bowtie 0.12.8 Bioinformatics zcluster Done, SMW clear, YH
bowtie2 2.0.0-beta7 Bioinformatics zcluster Done, SMW clear, YH
breakdancer 1.1_2011_02_21 Bioinformatics zcluster Done, SMW clear, YH
brownie 2.1.2 Bioinformatics zcluster Done, SMW clear, YH
BS Seeker Dec 113 Bioinformatics zcluster Done, SMW clear, YH
Burrows-Wheeler Aligner (BWA) 0.6.2 Bioinformatics zcluster Done, SMW clear, YH
cd-hit 4.5.6 Bioinformatics zcluster Done, SMW clear, YH
cdbfasta 04282012 Bioinformatics zcluster Done, SMW clear, YH
CEAS 1.0.2 Bioinformatics zcluster Done, SMW clear, YH
CEGMA 2.4.010312 Bioinformatics zcluster Done, SMW clear, YH
circos 0.62 Bioinformatics zcluster Done, SMW clear, YH
ClustalW 2.1 Bioinformatics zcluster Done, SMW clear, YH
Coding Potential Calculator 0.9-r2 Bioinformatics zcluster Done, SMW clear, YH 2/8 3:35pm
CONSEL v0.20 Bioinformatics zcluster Done, SMW clear, YH
cortex_con 0.04c Bioinformatics zcluster Done, SMW clear, YH
cortex_var 1.0.5.3 Bioinformatics zcluster Done, SMW clear, YH
Count 2010-04-02 Bioinformatics zcluster Done, SMW clear, YH
CREST 1.0 Bioinformatics zcluster Done, SMW clear, YH
ctrax 0.3.2 Other zcluster Done, SMW clear, YH
cufflinks 2.0.2 Bioinformatics zcluster Done, SMW clear, YH
cutadapt 1.1 Bioinformatics zcluster Done, SMW clear, YH
DLCoal 1.0 Bioinformatics zcluster Done, SMW clear, YH
drmma 0.5 Other zcluster Done, SMW clear, YH
ea-utils 1.1.2-537 Bioinformatics zcluster Done, SMW clear, YH
edena 3Dev120626 Bioinformatics zcluster Done, SMW clear, YH
EMBOSS 6.2.0 Bioinformatics zcluster clear, YH
emmix 1.3 Bioinformatics zcluster Done, SMW clear, YH
ESTscan 3.0.3 Bioinformatics zcluster Done, YH clear, YH
evm (EVidenceModeler) r2012-06-25 Bioinformatics zcluster Done, SMW clear, YH
ExaML 315576 Bioinformatics zcluster Done, SMW clear, YH
exonerate 2.2.0 Bioinformatics zcluster Done, SMW clear, YH
FAR 2.15 Bioinformatics zcluster Done, SMW clear, YH
FASTA 36 Bioinformatics zcluster Done, with Dead Links, SMW clear, YH
fasta format cleaner 1.0 Bioinformatics zcluster Done, YH clear, YH
FastQC 0.10.1 Bioinformatics zcluster Done, SMW clear, YH
fasttree 2.1.4 Bioinformatics zcluster Done, SMW clear, YH
FastX 0.0.13, 0.0.13.2 Bioinformatics zcluster Done, SMW clear, YH
FIRE 1.1 Bioinformatics zcluster Done, SMW clear, YH
FitModel 0.5.3 Bioinformatics zcluster Done, SMW clear, YH
FFTW 2.1.5, 3.3.0 Math Library zcluster Done, SHT clear, YH
FLASH 1.0.3 Bioinformatics zcluster Done, SMW clear, YH
GAMESS May2012R1 with XMVB 2.0. Chemistry zcluster
GAMESS-pcluster 2007 R6 Chemistry pcluster
GapFiller 1.11 Bioinformatics zcluster Done, SMW clear, YH
gatk 2.2-2-gf44cc4e Bioinformatics zcluster Done, SMW clear, YH
GAUSSIAN03 03 Chemistry pcluster
GAUSSIAN94 94 Chemistry pcluster
Gblocks 0.91b Bioinformatics zcluster Done, SMW clear, YH
GDB 7.0.1 Debugger zcluster Done, SHT clear, SHT
GeneMark genemark-ES 2.3e gGeneMark version 2.5m Bioinformatics zcluster Done, SMW clear, YH
Genome Phred version: 0.071220.c Bioinformatics zcluster Done, SMW clear, YH
GenomeMapper 0.4.3 (Version for SHORE/WMD3) Bioinformatics zcluster Done, SMW clear, YH
GenomeTools 1.3.9 Bioinformatics zcluster Done, SMW clear, YH
git 1.7.4.1, 1.7.9 Others zcluster
Glimmer 3.0.2 Bioinformatics zcluster JKP clear, YH
GlimmerHMM 3.0.1 Bioinformatics zcluster JKP clear, YH
gmap 2007-09-28 Bioinformatics zcluster DNP clear, YH
gmap-gsnap 2012-07-20 Bioinformatics zcluster DNP clear, YH
gnuplot 4.0, 4.6.0 Graphics zcluster Done, SHT clear, SHT
gprof 2.17 Profiler zcluster Done, SHT clear, SHT
gpu-blast 1.1 with ncbi-blast-2.2.25+ Bioinformatics zcluster JKP clear, YH
grace 5.1.22 Other zcluster
Gromacs 4.5.5 Chemistry zcluster Done, SHT clear, SHT
GSL 1.9, 1.15 Math Library zcluster Done, SHT clear, SHT
gss Bioinformatics zcluster skiped, DNP
HDF5 1.6.4, 1.8.9 Other zcluster
Hmmer 3.0 Bioinformatics zcluster DNP clear, YH
htseq 0.5.3p3 Bioinformatics zcluster JKP clear, YH
igb 6.7.3 Bioinformatics zcluster DNP clear, YH
IGV 2.1.23 Bioinformatics zcluster JKP clear, YH
IMa May 06 Bioinformatics pcluster DNP clear, YH
indel-Seq-Gen 2.02 Bioinformatics zcluster JKP clear, YH
InStruct 3.2.09 Bioinformatics zcluster JKP clear, YH
iprscan (InterProScan) 5.0 CR2 Bioinformatics zcluster DNP clear, YH
iscan 1.0.0 Bioinformatics zcluster JKP clear, YH
Jellyfish 1.1.5 Bioinformatics zcluster DNP
k-link 03 27, 2009 Bioinformatics zcluster DNP
LAPACK 3.0, 3.4.2 Math Library zcluster Done, SHT clear, SHT
LASTZ 1.03.02 Bioinformatics zcluster JKP
LDDist 1.3.2 Bioinformatics zcluster DNP
libsequence 1.7.4 Bioinformatics zcluster JKP
LLVM-Clang 3.1 Compiler zcluster
lsa 11182011 Bioinformatics zcluster DNP
macs 1.4.2 Bioinformatics zcluster DNP
mafft 6.864b Bioinformatics zcluster JKP
maker 2.10 Bioinformatics zcluster DNP
Maple-pcluster 10.06 Other pcluster
MAQ 0.7.1 Bioinformatics zcluster JKP
Mathematica 5.2 Other pcluster
MatLab R2012a (7.14.0.739) Other zcluster
MCL 12-135 Bioinformatics zcluster DNP
MEAD 2.2.9 Chemistry zcluster
megan 4.67.2 Bioinformatics zcluster JKP
MEME 4.8.1 Bioinformatics zcluster DNP
Migrate 3.0.3 Bioinformatics zcluster JKP
Minia 1.4683 Bioinformatics zcluster JKP
MIRA 3.9.9 Bioinformatics zcluster DNP
MKL 2013 Math Library zcluster working, SHT
MOTECC qmdcp 90 Chemistry zcluster
MOTECC qmdcp pcluster 90 Chemistry pcluster
MOTHUR 1.28.0 Bioinformatics zcluster DNP
mpi4py 1.3 Utilities zcluster
mpiblast 1.6.0 Bioinformatics zcluster JKP
MrBayes 3.1.2 Bioinformatics zcluster DNP
mrfast 2.5.0.4 Bioinformatics zcluster JKP
MSA 3.8.1b Bioinformatics zcluster DNP
MUSCLE 3.8.31 Bioinformatics zcluster JKP
MyScanACE 04232012 Bioinformatics zcluster JKP
NAMD 2.9 Chemistry zcluster
NAMD-pcluster 2.6b2, 2.7b1 Chemistry pcluster
NCBI Blast 2.2.26 Bioinformatics zcluster Done, YH clear, YH
NCBI Blast + 2.2.26 Bioinformatics zcluster DNP clear, YH
ncbi blast parsers Bioinformatics zcluster JKP, missing information clear, YH
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 JKP clear, YH
Ngsutils 0.5.0c Bioinformatics zcluster YH clear, YH
NH PhyloBayes 0.2.3 Bioinformatics zcluster JKP clear, YH
nhPhyML 01/2012 Bioinformatics zcluster DNP clear, YH
NovelSeq 1.0.2 Bioinformatics zcluster DNP clear, YH
NovoAlign 2.07 Bioinformatics zcluster JKP clear, YH
numexp 1.4.2 Other zcluster
NWCHEM 4.7 Chemistry pcluster
Oases 0.2.02 Bioinformatics zcluster JKP clear, YH
opal 2.0.0 Bioinformatics zcluster JKP clear, YH
Open Babel 2.3.1 Chemistry zcluster
OpenBUGS 3.2.2 Statistics zcluster
OpenCV 2.3.1 Other zcluster
OSPREY 2.0 Bioinformatics zcluster JKP clear, YH
p4 r231 Bioinformatics zcluster JKP clear, YH
pagan 0.39 Bioinformatics zcluster JKP clear, YH
PAML 4.4 Bioinformatics zcluster JKP clear, YH
pandaseq 2.0 Bioinformatics zcluster JKP clear, YH 2/8 3:35pm
Papara_nt 2.1.2 Bioinformatics zcluster JKP clear, YH
PASHA 1.0.6 Bioinformatics zcluster JKP clear, YH
PeakSplitter 1.0 Bioinformatics zcluster JKP clear, YH
pebl 1.01 zcluster
Perl 5.14.1 Programming Language zcluster Done, SHT
Pfam_scan 04282012 Bioinformatics zcluster JKP clear, YH
pftools 2.3.5 Bioinformatics zcluster JKP clear, YH
PGDBG 12.10 Debugger zcluster Done, SHT clear, SHT
PGPROF 12.10 Profiler zcluster Done, SHT clear, SHT
phred/phrap/conced Bioinformatics zcluster JKP, not enough information clear, YH
Phyldog Bioinformatics zcluster Done, SHT clear, SHT
PhyloBayes 3.3b Bioinformatics zcluster JKP clear, YH
PHYML 20110919 Bioinformatics zcluster JKP clear, YH
picard 1.62 Bioinformatics zcluster JKP clear, YH
pileup 0.6 Bioinformatics zcluster clear, YH
prank 100802 Bioinformatics zcluster JKP clear, YH
Primer3 2.3.4 Bioinformatics zcluster JKP clear, YH
pysam 0.6 Bioinformatics zcluster JKP clear, YH
PyTables 2.3.1 Other zcluster
Python 2.4.3, 2.7.2, 3.3.0 Programming Language zcluster Done, SHT
Qiime 1.6.0 Bioinformatics zcluster JKP clear, YH
QTL Cartographer 1.17j Bioinformatics zcluster JKP clear, YH
quake 0.3.4 Bioinformatics zcluster JKP clear, YH
Quantum Espresso 5.0.2 Chemistry zcluster working, JKP
R 2.14.0, 2.15.0, 2.15.2 Statistics zcluster Done, SHT clear, SHT
R-pcluster 1.9.1, 2.1.1, 2.4.0 pcluster
RAxML 04/26/2012 Bioinformatics zcluster JKP clear, YH
RAxML-Light 1.0.5 Bioinformatics zcluster JKP clear, YH
Ray 1.6.1-0 Bioinformatics zcluster skipped, JKP
RCCBatchBlast 5.0 Bioinformatics zcluster JKP clear, YH
RCCBatchBlastPlus 1.0 Bioinformatics zcluster done, YH clear, YH
RECON 1.05 Bioinformatics zcluster JKP clear, YH
Repeatmasker 3.3 Bioinformatics zcluster JKP clear, YH
RepeatScout 1.05 Bioinformatics zcluster JKP clear, YH
riboPicker 0.4.3 Bioinformatics zcluster JKP clear, YH
RMBlast 2.2.27 Bioinformatics zcluster JKP clear, YH
Rmpi 0.5-9 Statistics zcluster JKP
RNAz 2.1 Bioinformatics zcluster JKP clear, YH
rnnotator 2.4.12 Bioinformatics zcluster JKP clear, YH
Roche 2.6 Bioinformatics zcluster JKP, dead link in description clear, YH
RSAT (RSA-tools) 1.0 Bioinformatics zcluster JKP clear, YH
RSEM 1.1.21, 1.2.0 Bioinformatics zcluster JKP clear, YH
RUM 1.11 Bioinformatics zcluster JKP, Verify GACRC Support Form link clear, YH
Sage 3.1.1, 3.4.1 Other zcluster skipped, JKP
samtools 0.1.18 Bioinformatics zcluster JKP clear, YH
SAS 9.1 Statistics zcluster JKP
SATé 2.2.4 Bioinformatics zcluster clear, YH
SEQuel 1.0.2 Bioinformatics zcluster JKP clear, YH
SHE-RA 012012 Bioinformatics zcluster JKP, Dead links clear, YH
SHORE 0.8 Bioinformatics zcluster JKP clear, YH
sickle 1.200 Bioinformatics zcluster JKP clear, YH
SiZer 07022012 Bioinformatics zcluster JKP clear, YH
slclust 04282012 Bioinformatics zcluster JKP clear, YH
SNAP 2010-7-28 Bioinformatics zcluster JKP clear, YH
snow 0.3-8 Statistics zcluster JKP
snowhite 1.1.4 Bioinformatics zcluster JKP clear, YH
snpEff 2_0_5d Bioinformatics zcluster JKP clear, YH 2/7 8:30 am YH
SOAPdenovo 1.05 Bioinformatics zcluster JKP clear, YH
SOAPdenovo-trans 1.01 Bioinformatics zcluster JKP clear, YH
SOAPdenovo2 r223 Bioinformatics zcluster JKP clear, YH
SomaticCall 42811 Bioinformatics zcluster JKP clear, YH
spimap 1.1 Bioinformatics zcluster JKP clear, YH
SpliceGrapher 0.2.0 Bioinformatics zcluster JKP clear, YH
SSAHA2 2.5.5 Bioinformatics zcluster JKP clear, YH
SSPACE 2.0 Bioinformatics zcluster JKP clear, YH
stacks 0.9993, 0.9996 Bioinformatics clear, YH
STEM 2.0 Bioinformatics zcluster JKP clear, YH
strauto 0.3.1 Bioinformatics zcluster JKP clear, YH
structure 2.3.3 Bioinformatics zcluster JKP clear, YH
SVDetect r0.7m Bioinformatics zcluster JKP ? clear, YH
SWIG 2.0.5 Utilities zcluster JKP
T-Coffee 9.03.r1318 Bioinformatics zcluster JKP clear, YH
tabix 0.2.5 Bioinformatics zcluster JKP clear, YH
tagdust 1.12 Bioinformatics zcluster JKP ? clear, YH
tassel 4.0 Bioinformatics zcluster JKP clear, YH
tgicl 2.1 Bioinformatics zcluster JKP clear, YH
TIGER 1.02 Bioinformatics zcluster JKP clear, YH
tophat 2.0.5 Bioinformatics zcluster JKP clear, YH
Tracer v 1.5 Bioinformatics zcluster JKP clear, YH
Trinity r2012-10-05 Bioinformatics zcluster JKP clear, YH
UNAFold 3.8 Bioinformatics zcluster JKP ? clear, YH
usearch v6.0.30 Bioinformatics zcluster JKP clear, YH
vcftools 0.1.10 Bioinformatics zcluster Done, JKP clear, YH
velvet 1.2.01 Bioinformatics zcluster JKP clear, YH
VelvetOptimiser 2.2.4 Bioinformatics zcluster JKP clear, YH
ViennaRNA 1.8.5 Bioinformatics zcluster JKP clear, YH
virtualenv 1.8.1 Other zcluster YH clear, YH
vmatch 2.1.6 Bioinformatics zcluster JKP clear, YH
VMD 1.9.1 Chemistry zcluster JKP, skipped
wigToBigWig v 4 Bioinformatics zcluster JKP clear, YH
WISE2 2.2.0 Bioinformatics zcluster JKP clear, YH
WU Blast 2.2.6 Bioinformatics zcluster JKP clear, YH
yasra 2.3 Bioinformatics zcluster JKP clear, YH
Zz-example 0.0 Bioinformatics zcluster example for bioinformatics YH
Zz-template 0.0 Bioinformatics zcluster Template for bioinformatics YH
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