Software-old

Installed Software List

Last updated 2013-01-14.

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

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		stats
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
Qlogic Infiniband
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	2012		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