Software-old

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Installed Software List

Last updated 2013-01-30.

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
Artemis Release 8 Bioinformatics rcluster
Bali-phy-Altix 1.9.8 Bioinformatics Altix
Bali-phy-rcluster 1.9.8 Bioinformatics rcluster
BEAST 1.7.2 Bioinformatics zcluster
BEST Bayesian 2.3.1 Bioinformatics
BEST Binding 1.0 Bioinformatics rcluster
Bioconductor 1.9 (compiled with R-2.4.0) Bioinformatics rcluster
BioPerl-altix 1.4 Bioinformatics Altix
BioPerl 1.61 Bioinformatics zcluster
BioPython 1.58 Bioinformatics zcluster
NCBI Blast-Altix 2.2.20 is the last updated. older versions are also available. Bioinformatics Altix
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
CAP3-Altix Date - 04/15/2005 Bioinformatics Altix
CAP3-rcluster IOB Date : 04/15/2005 Bioinformatics rcluster
ClustalW-Altix 1.8.3 Bioinformatics Altix
ClustalW 2.1 Bioinformatics zcluster
CONSEL v0.20 Bioinformatics zcluster
EMBOSS-Altix 6.0.1 (updated at 02/09/2008) Bioinformatics Altix
EMBOSS-rcluster 6.2.0 (updated at 04/17/2010) Bioinformatics rcluster
FASTA 36 Bioinformatics zcluster
FIRE 1.1 Bioinformatics zcluster
FitModel 0.5.3 Bioinformatics zcluster
Gblocks-rcluster 0.91b Bioinformatics rcluster
GCG (Wisconsin Package) 11.0 Bioinformatics rcluster
Genezilla 1.0 Bioinformatics rcluster
Genome-Altix Phred version: 0.020425.c
Genome Phred version: 0.071220.c
Hmmer-Altix v3.0.a1
Hmmer 3.0 Bioinformatics
IMa May 06 Bioinformatics
indel-Seq-Gen 2.02 Bioinformatics
iprscan (InterProScan) 5.0 CR2 Bioinformatics
LUCY-Altix 1.19 Bioinformatics Altix
LUCY-rcluster 1.19 Bioinformatics
MDscan 2004 Bioinformatics rcluster
MEME 4.8.1 Bioinformatics zcluster
Migrate 3.0.3 Bioinformatics
MrBayes-altix 3.1.2 Bioinformatics Altix
MrBayes 3.1.2 Bioinformatics
MSBlast 2003 Bioinformatics rcluster
MUMmer 3.22 Bioinformatics rcluster
MUSCLE-Altix 3.6 Bioinformatics Altix
MUSCLE 3.8.31 Bioinformatics zcluster
PAML Latest version 4.4 Bioinformatics zcluster
Pfam_scan 04282012 Bioinformatics zcluster
pfamDNASearch 1.5 Bioinformatics rcluster
pftools 2.3.5 Bioinformatics zcluster
PHYLIP 3.6 Bioinformatics rcluster
PHYML 20110919 Bioinformatics
PolyBayes-Altix 3.0 Bioinformatics Altix
PolyBayes-rcluster 3.0 Bioinformatics rcluster
PSORTb 3.0.2 Bioinformatics rcluster
RAxML 04/26/2012 Bioinformatics zcluster
RECON 1.05 Bioinformatics rcluster
RepeatFinder n/a Bioinformatics rcluster
Repeatmasker 3.3 Bioinformatics zcluster
RepeatScout 1.05 Bioinformatics zcluster
Reputer 2.74 Bioinformatics rcluster
SSAHA2 1.0.9 Bioinformatics rcluster
STEM 2.0 Bioinformatics zcluster
SVM_Light 6.01 Bioinformatics rcluster
T-Coffee-rcluster v 7.54 Bioinformatics rcluster
Tracer v 1.5 Bioinformatics zcluster
WISE2 2.2.0 Bioinformatics zcluster
WU Blast-Altix 2.2.6 Bioinformatics rcluster
3D_DOCK 2.0 Computational Chemistry pcluster
AMBER-pcluster 8 Computational Chemistry
GAMESS-pcluster 2007 R6
GAUSSIAN03 03 Computational Chemistry pcluster
GAUSSIAN94 94 Computational Chemistry pcluster
Gromacs-rcluster 3.3.3 4.0 and 4.5.3 Computational Chemistry
MOTECC qmdcp -pcluster 90 Computational Chemistry pcluster
NAMD-rcluster 2.6 2.6b2 2.7b1
NWCHEM 4.7 Computational Chemistry pcluster
OpenMX-rcluster 3.4.4v Computational Chemistry rcluster
VMD-rcluster 1.8.4 Computational Chemistry rcluster
XPLOR-NIH -rcluster 2.15 Computational Chemistry rcluster
X!!Tandem-rcluster Computational Chemistry rcluster
Cddlib 0.94 Other rcluster
Gfan 0.3 Other rcluster
Macaulay2 2-1.1 Other rcluster
Maple-pcluster 10.06 Other pcluster
Mathematica 5.2 Other pcluster
MatLab R2012a (7.14.0.739) Other zcluster
NETCDF-pcluster 3.5.1, 3.6.2 Other
polymake 2.3 and alpha 2.9.5 Other rcluster
Sage 3.1.1, 3.4.1 Other
LinBUGS-rcluster uses OpenBUGS 2.2.0 Statistics rcluster
R-pcluster 1.9.1, 2.1.1, 2.4.0
R-rcluster 2.4.0, 2.5.1, 2.7.0
SAS 9.1 Statistics
Bl2seq Bioinformatics
Blastall Bioinformatics zcluster
BLASTCLUST Bioinformatics
BLAST Databases
Blastpgp Bioinformatics
fastacmd
Formatdb
MEGABLAST
Arabidopsis Database rcluster
Arb
Bacteria NCBI
COG
NCBI_database Bioinformatics zcluster
gss Bioinformatics
FISH
Homo_sapien
htgs
KEGG
Medicago
Populus Rcluster
Refseq
Rice TIGR
Roseobacter
Silva
Sus_scrofa
Uniprot
Uniref
wublast Bioinformatics
WU Blast 2.2.6 Bioinformatics zcluster
AMBER-rcluster 8, 10 Computational Chemistry
CodonW Last Update : 2009-Oct-14. Bioinformatics rcluster
ITK 3.16.0 Others rcluster
VTK 5.4.2 Others rcluster
FSL 4.1.4 Others rcluster
MFOLD 3.4 Bioinformatics rcluster
NAMD-pcluster 2.6b2, 2.7b1 Computational Chemistry
AlignACE Last Update : 2004 Bioinformatics rcluster
NovoAlign 2.07 Bioinformatics zcluster
MAQ 0.7.1 Bioinformatics zcluster
RepeatModeler 1.0.5 Bioinformatics rcluster
Tandem Repeats Finder 404 Bioinformatics rcluster
go-perl 0.10 Bioinformatics rcluster
STAMP 1.10 Bioinformatics rcluster
MIRA 3.9.9 Bioinformatics zcluster
consensus-v6c Version 6c. Bioinformatics rcluster
pebl 1.01 installed for Python 2.6.2
ESTScan 2-2.1 Bioinformatics rcluster
Burrows-Wheeler Aligner (BWA) 0.6.2\
maize Database rcluster
RCAC Awards 1.3M+ CPU Hours
tophat 2.0.5 Bioinformatics zcluster
boxshade v3.31 C Bioinformatics Rcluster
pfam 26.0 database zcluster
128GB Dell Replaces 32GB Altix
ncbi blast parsers Bioinformatics zcluster
Newbler 2.6 Bioinformatics zcluster
mpi4py -rcluster 1.2.1 Utilities rcluster
MOTHUR-rcluster 1.8.0, 1.9.0, 1.12.0
SUPERSPLAT 1.0 Bioinformatics rcluster
SHRIMP 2.1.1d Bioinformatics rcluster
velvet 1.2.01 Bioinformatics zcluster
bowtie 0.12.8 Bioinformatics zcluster
MSPcrunch 2.5 Bioinformatics rcluster
Qiime-rcluster 1.3.0 Bioinformatics rcluster
Mono 2.4.3 Utilities rcluster
Maple-rcluster 14 Other rcluster
ABINIT-rcluster 6.0.4 Computational Chemistry rcluster
miRanda 3.3a Bioinformatics rcluster
pplacer 1.0 Bioinformatics rcluster
PSLDoc v2010-01 Bioinformatics rcluster
QTL Cartographer 1.17j Bioinformatics zcluster
ViennaRNA 1.8.5 Bioinformatics zcluster
RNAz 2.1 Bioinformatics zcluster
LocARNA 1.5.2 Bioinformatics rcluster
ngs_backbone 1.0.0 Bioinformatics rcluster
SeqClean 1.0 Bioinformatics rcluster
MCL-rcluster 10-148 Bioinformatics rcluster
Oases 0.2.02 Bioinformatics rcluster
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
CELLO 2.6 Bioinformatics rcluster
twinScan/n-Scan 4.1.2 Bioinformatics rcluster
IDEG 6.0 Bioinformatics rcluster
KiNG 2.17 Bioinformatics rcluster
fasta format cleaner 1.0 Bioinformatics rcluster
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
tRNAscan-SE 1.23 Bioinformatics rcluster
NCBI Blast + 2.2.26 is the last updated Bioinformatics rcluster
LASTZ 1.03.02 Bioinformatics zcluster
Multiz 012109 Bioinformatics rcluster
plink 1.07 Bioinformatics rcluster
iParameterEstimation (iPE) 0.3.1 Bioinformatics Rcluster
carma-rcluster 1.1 Computational Chemistry rcluster
samtools 0.1.18 Bioinformatics zcluster
Archival Disk Storage Service
OpenBUGS-rcluster 3.1.2 Statistics rcluster
git 1.7.4.1, 1.7.9 Others
PIIM 2.0.1 Bioinformatics rcluster
count-rcluster 032011 Bioinformatics rcluster
kaas 100218 Bioinformatics rcluster
BS Seeker download at Dec 113 Bioinformatics
LDhat 2.1 Bioinformatics rcluster
mafft 6.864b Bioinformatics zcluster
opal 2.0.0 Bioinformatics zcluster
SATé 2.2.4 Bioinformatics zcluster
MOTECC qmdcp 90 Computational Chemistry zcluster
scipio 1.4 Bioinformatics rcluster
spaln 1.4.5 Bioinformatics rcluster
FrameDP 1.0.3 Bioinformatics rcluster
Codon Usage 1.00 Bioinformatics rcluster
mVISTA 1.4.26 Bioinformatics rcluster
AVID 2.1 Bioinformatics rcluster
TreeBeST 1.9.2 Bioinformatics rcluster
PrIMETV 1.5.6 Bioinformatics rcluster
Ray 1.4.0, 1.6.1-0 Bioinformatics
LAGAN 2.0 Bioinformatics rcluster
SRA 2.1.7 Bioinformatics rcluster
Trinity Versions r2012-10-05 Bioinformatics zcluster
k-link 03 27, 2009 Bioinformatics
RBR 0.8.6 Bioinformatics rcluster
BFast 0.6.5a Bioinformatics rcluster
FastX Version 0.0.13, 0.0.13.2 Bioinformatics
MyScanACE 04232012 Bioinformatics zcluster
wcdest 0.6.3 Bioinformatics rcluster
Quantum Espresso-rcluster 4.3.2 Computational Chemistry rcluster
mosaik Mosaik 1.1.0021    Bioinformatics rcluster
primegsr 1.0 Bioinformatics rcluster
FAR (Flexible Adapter Remover) 2.0 Bioinformatics rcluster
topHat-fusion-rcluster 0.1.0 Bioinformatics rcluster
gatk 2.2-2-gf44cc4e Bioinformatics zcluster
gatk-rcluster Bioinformatics rcluster
splign 1.39.8 Bioinformatics rcluster
socs 2.1.1 Bioinformatics rcluster
gfftosam (BaseQV) 1.0.1 Bioinformatics rcluster
MaTogff 0.2.06 Bioinformatics rcluster
breakdancer 1.1_2011_02_21 Bioinformatics zcluster
CREST 1.0 Bioinformatics zcluster
SOAPdenovo 1.05 Bioinformatics zcluster
SEQuel 1.0.2 Bioinformatics zcluster
TreeView X 0.5.1 Bioinformatics rcluster
soap2 2.21 Bioinformatics rcluster
cd-hit 4.5.6 Bioinformatics zcluster
I-TASSER 1.1 Bioinformatics rcluster
I-TASSER 1.1 Bioinformatics rcluster
inteRNA 3.3 Bioinformatics rcluster
RactIP 0.0.2 Bioinformatics rcluster
ABySS-rcluster 1.3.1 Bioinformatics rcluster
amos 3.1.0 Bioinformatics zcluster
lsa 11182011 Bioinformatics zcluster
SNVMix2 0.11.8-r4 Bioinformatics rcluster
AmpliconNoise 1.25 Bioinformatics rcluster
mrfast 2.5.0.4 Bioinformatics zcluster
shorha 0.5.1 Bioinformatics rcluster
tassel 4.0 Bioinformatics zcluster
nupack 3.0 Bioinformatics rcluster
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
STEM-rcluster Bioinformatics rcluster
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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