Software-old: Difference between revisions

Revision as of 08:15, 21 March 2013

Installed Software List

Last updated 2013-03-21.

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0-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

Name	Version	Category	Cluster
3D_DOCK	2.0	Chemistry	Pcluster
454 Software		Bioinformatics	Zcluster
aaarf	1.0.0	Bioinformatics	Zcluster
ABINIT	6.12.1	Chemistry	Zcluster
ABySS	1.3.4	Bioinformatics	Zcluster
Admixture	1.22	Bioinformatics	Zcluster
ALLPATHS-LG	44254	Bioinformatics	Zcluster
AMBER	11, 12	Chemistry	Zcluster
AMBER-pcluster	8, 10	Chemistry	Pcluster
amos	3.1.0	Bioinformatics	Zcluster
AmpliconNoise	1.25	Bioinformatics	Zcluster
ARB	5.3	Bioinformatics	Zcluster
Aspera	3.1.0.67054	Other	Zcluster
AUGUSTUS	2.5.5	Bioinformatics	Zcluster
bam2fastq	1.1.0	Bioinformatics	Zcluster
BEAST	1.7.2	Bioinformatics	Zcluster
BEDTools	2.16.2	Bioinformatics	Zcluster
BEST	2.3.1	Bioinformatics	Zcluster
bfast	2.3.1	Bioinformatics	Zcluster
Bio++	2.0.3	Bioinformatics	Zcluster
Bioconductor	2.11	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
BLAS	3.0	Math Library	Zcluster
Blat	3.5	Bioinformatics	Zcluster
BMGE	1.1	Bioinformatics	Zcluster
Boost	1.47.0, 1.48.0	Library	Zcluster
bowtie	0.12.8	Bioinformatics	Zcluster
bowtie2	2.1.0	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
cap3	10/2011	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
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
CUDA	4.0.17, 4.2.9, 5.0.35	Programming	Zcluster
cufflinks	2.0.2	Bioinformatics	Zcluster
cutadapt	1.1	Bioinformatics	Zcluster
dnasam	20100621	Bioinformatics	Zcluster
demuxipy	1.0	Bioinformatics	Zcluster
DLCoal	1.0	Bioinformatics	Zcluster
drmma	0.5	Other	Zcluster
ea-utils	1.1.2-537	Bioinformatics	Zcluster
edena	3Dev120626	Bioinformatics	Zcluster
editag	1.1	Bioinformatics	Zcluster
EMBOSS	6.5.7	Bioinformatics	Zcluster
emmix	1.3	Bioinformatics	Zcluster
ESTscan	3.0.3	Bioinformatics	Zcluster
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
fasta format cleaner	1.0	Bioinformatics	Zcluster
fastphase	1.4.0	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
FitModel	0.5.3	Bioinformatics	Zcluster
FFTW	2.1.5, 3.3.0, 3.3.3	Math Library	Zcluster
FLASH	1.0.3	Bioinformatics	Zcluster
Freebayes	0.9.6	Bioinformatics	Zcluster
GAMESS	May2012R1 with XMVB 2.0.	Chemistry	Zcluster
GAMESS-pcluster	Mar. 24, 2007 R6, Apr.11, 2008 R1, Aug.11, 2011	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
GDB	7.0.1	Debugger	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	Other	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
GNU Compilers	4.1.2, 4.4.6, 4.5.3, 4.7.1	Compiler	Zcluster
gnuplot	4.0, 4.6.0	Graphics	Zcluster
gprof	2.17	Profiler	Zcluster
gpu-blast	1.1 with ncbi-blast-2.2.25+	Bioinformatics	Zcluster
grace	5.1.22	Graphics	Zcluster
Gromacs	4.5.5	Chemistry	Zcluster
GSL	1.9, 1.15	Math Library	Zcluster
gss		Bioinformatics	Zcluster
Hapmix	2	Bioinformatics	Zcluster
HDF5	1.6.4, 1.8.9	Library	Zcluster
Hmmer	3.0	Bioinformatics	Zcluster
htseq	0.5.3p3	Bioinformatics	Zcluster
IBM XL C/C++	7.0	Compiler	Pcluster
IBM XL Fortran	9.1	Compiler	Pcluster
igb	6.7.3	Bioinformatics	Zcluster
IGV	2.1.23	Bioinformatics	Zcluster
IMa	May 06, 2009	Bioinformatics	Pcluster
indel-Seq-Gen	2.02	Bioinformatics	Zcluster
InStruct	3.2.09	Bioinformatics	Zcluster
Intel Compilers	2013	Compiler	Zcluster
iprscan (InterProScan)	5.0 RC5	Bioinformatics	Zcluster
iscan	1.0.0	Bioinformatics	Zcluster
JasPer	1.900.1	Other	Zcluster
Jellyfish	1.1.5	Bioinformatics	Zcluster
JModelTest	2.1.2	Bioinformatics	Zcluster
k-link	03 27, 2009	Bioinformatics	Zcluster
LAPACK	3.0, 3.4.2	Math Library	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
maker	2.10	Bioinformatics	Zcluster
Maple	16	Other, Programming, Graphics	Zcluster
Maple-pcluster	10.06	Other, Programming, Graphics	Pcluster
MAQ	0.7.1	Bioinformatics	Zcluster
Mathematica	5.2	Other, Programming , Graphics	Pcluster
MatLab	R2012a (7.14.0.739)	Other, Programming, Graphics	Zcluster
MCL	12-135	Bioinformatics	Zcluster
MEAD	2.2.9	Chemistry	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
MKL	11.0	Math Library	Zcluster
MONO	3.0.3	Other, Programming	Zcluster
MOSAIK	2.1.73	Bioinformatics	Zcluster
MOTECC qmdcp	90	Chemistry	Zcluster
MOTECC qmdcp	90	Chemistry	Pcluster
MOTHUR	1.28.0	Bioinformatics	Zcluster
MP-EST	1.3	Programming	Zcluster
mpi4py	1.3	Programming	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
NCBI Blast +	2.2.26	Bioinformatics	Zcluster
ncbi blast parsers		Bioinformatics	Zcluster
NETCDF	3.6.3, 4.1.3	Library	Zcluster
NETCDF-pcluster	3.5.1, 3.6.2	Library	Pcluster
netlogo	5.0	Other	Zcluster
Newbler	2.6	Bioinformatics	Zcluster
Newick-utils	1.6	Bioinformatics	Zcluster
Ngsutils	0.5.0c	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
NPUTE	v1	Bioinformatics	Zcluster
numexp	1.4.2	Other	Zcluster
NWCHEM	4.7	Chemistry	Pcluster
Oases	0.2.02	Bioinformatics	Zcluster
opal	2.0.0	Bioinformatics	Zcluster
Open Babel	2.3.1	Chemistry	Zcluster
OpenBUGS	3.2.2	Statistics	Zcluster
OpenCL	1.0, 1.1	Programming	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
ParseRNAseq	1.0	Bioinformatics	Zcluster
PASHA	1.0.6	Bioinformatics	Zcluster
PeakSplitter	1.0	Bioinformatics	Zcluster
Perl	5.14.1	Programming	Zcluster
perM	0.4.0	Bioinformatics	Zcluster
Pfam_scan	04282012	Bioinformatics	Zcluster
pftools	2.3.5	Bioinformatics	Zcluster
PGDBG	12.10	Debugger	Zcluster
PGI Compilers	2010, 2011, 2012	Compiler	Zcluster
PGPROF	12.10	Profiler	Zcluster
phred/phrap/conced		Bioinformatics	Zcluster
Phyldog		Bioinformatics	Zcluster
PhyloBayes	3.3b	Bioinformatics	Zcluster
PhyloBayes-MPI	1.3b	Bioinformatics	Zcluster
Phylip	3.69	Bioinformatics	Zcluster
PHYML	20110919	Bioinformatics	Zcluster
picard	1.62	Bioinformatics	Zcluster
pileup	0.6	Bioinformatics	Zcluster
pindel	0.2.4t	Bioinformatics	Zcluster
plink	0.2.4t	Bioinformatics	Zcluster
prank	100802	Bioinformatics	Zcluster
Primer3	2.3.4	Bioinformatics	Zcluster
pysam	0.6	Bioinformatics	Zcluster
PyTables	2.3.1	Other	Zcluster
Python	2.4.3, 2.7.2, 3.3.0	Programming	Zcluster
Qiime	1.6.0	Bioinformatics	Zcluster
QTL Cartographer	1.17j	Bioinformatics	Zcluster
quake	0.3.4	Bioinformatics	Zcluster
Quantum Espresso	4.3.2, 5.0.2	Chemistry	Zcluster
R	2.14.0, 2.15.0, 2.15.2	Statistics	Zcluster
R-pcluster	1.9.1, 2.1.1	Statistics	Pcluster
RAxML	04/26/2012	Bioinformatics	Zcluster
RAxML-Light	1.0.5	Bioinformatics	Zcluster
RCCBatchBlast	5.0	Bioinformatics	Zcluster
RCCBatchBlastPlus	1.0	Bioinformatics	Zcluster
RECON	1.05	Bioinformatics	Zcluster
Repeatmasker	3.3	Bioinformatics	Zcluster
Reptile	1.1	Bioinformatics	Zcluster
RepeatScout	1.05	Bioinformatics	Zcluster
riboPicker	0.4.3	Bioinformatics	Zcluster
RIP	4	Other	Zcluster
RMBlast	2.2.27	Bioinformatics	Zcluster
Rmpi	0.5-9, 0.6-1	Programming	Zcluster
RNAz	2.1	Bioinformatics	Zcluster
rnnotator	2.4.12	Bioinformatics	Zcluster
Roche	2.6	Bioinformatics	Zcluster
RSAT (RSA-tools)	1.0	Bioinformatics	Zcluster
RSEM	1.2.3	Bioinformatics	Zcluster
RUM	1.11	Bioinformatics	Zcluster
samtools	0.1.18	Bioinformatics	Zcluster
SAS	9.1	Statistics	SAS Server
SATé	2.2.7	Bioinformatics	Zcluster
SEQuel	1.0.2	Bioinformatics	Zcluster
SHE-RA	012012	Bioinformatics	Zcluster
SHORE	0.8	Bioinformatics	Zcluster
SHOREmap	2.0	Bioinformatics	Zcluster
sickle	1.200	Bioinformatics	Zcluster
SiZer	07022012	Bioinformatics	Zcluster
slclust	04282012	Bioinformatics	Zcluster
SNAP	2010-7-28	Bioinformatics	Zcluster
snow	0.3-8, 0.3-10	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	0.2.1	Bioinformatics	Zcluster
Sputnik	XX	Bioinformatics	Zcluster
SSAHA2	2.5.5	Bioinformatics	Zcluster
SSAKE	v3-8	Bioinformatics	Zcluster
SSPACE	2.0	Bioinformatics	Zcluster
stacks	0.99994	Bioinformatics	Zcluster
STEM	2.0	Bioinformatics	Zcluster
strauto	0.3.1	Bioinformatics	Zcluster
structure	2.3.3	Bioinformatics	Zcluster
SVDetect	r0.7m	Bioinformatics	Zcluster
SWIG	2.0.5	Programming	Zcluster
T-Coffee	9.03.r1318	Bioinformatics	Zcluster
tabix	0.2.5	Bioinformatics	Zcluster
tagdust	1.12	Bioinformatics	Zcluster
TAPDANCE	03/20/2013	Bioinformatics	Zcluster
tassel	4.0	Bioinformatics	Zcluster
tgicl	2.1	Bioinformatics	Zcluster
TIGER	1.02	Bioinformatics	Zcluster
tophat	2.0.5	Bioinformatics	Zcluster
trans-abyss	1.4.4	Bioinformatics	Zcluster
Tracer	v 1.5	Bioinformatics	Zcluster
Trinity	r2013-02-25	Bioinformatics	Zcluster
UNAFold	3.8	Bioinformatics	Zcluster
UPP	2.0	Other	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
virtualenv	1.8.1	Other	Zcluster
vmatch	2.1.6	Bioinformatics	Zcluster
VMD	1.9.1	Chemistry	Zcluster
wigToBigWig	v 4	Bioinformatics	Zcluster
WISE2	2.2.0	Bioinformatics	Zcluster
WPS	3.4.1	Other	Zcluster
WRF	3.4.1	Other	Zcluster
WU Blast	2.2.6	Bioinformatics	Zcluster
yasra	2.3	Bioinformatics	Zcluster

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 | [[BEST]] || 2.3.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Zcluster|Zcluster]] || [[File:Up20.png|20px|link=#top]]
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+| [[bfast]] || 2.3.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Zcluster|Zcluster]] || [[File:Up20.png|20px|link=#top]]
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 | [[Bio++]] || 2.0.3 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Zcluster|Zcluster]] || [[File:Up20.png|20px|link=#top]]
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 | [[FLASH]] || 1.0.3 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Zcluster|Zcluster]] || [[File:Up20.png|20px|link=#top]]
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+| [[Freebayes]] || 0.9.6 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Zcluster|Zcluster]] || [[File:Up20.png|20px|link=#top]]
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 | <span id="G"></span>[[GAMESS]] || May2012R1 with XMVB 2.0. || [[:Category:Chemistry|Chemistry]] || [[:Category:Zcluster|Zcluster]] || [[File:Up20.png|20px|link=#top]]
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 | [[Perl]] || 5.14.1 || [[:Category:Programming|Programming]] || [[:Category:Zcluster|Zcluster]] || [[File:Up20.png|20px|link=#top]]
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+| [[perM]] || 0.4.0 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Zcluster|Zcluster]] || [[File:Up20.png|20px|link=#top]]
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 | [[Pfam_scan]] || 04282012 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Zcluster|Zcluster]] || [[File:Up20.png|20px|link=#top]]
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 | [[pindel]] || 0.2.4t || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Zcluster|Zcluster]] || [[File:Up20.png|20px|link=#top]]
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+| [[plink]] || 0.2.4t || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Zcluster|Zcluster]] || [[File:Up20.png|20px|link=#top]]
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 | [[prank]] || 100802 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Zcluster|Zcluster]] || [[File:Up20.png|20px|link=#top]]
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 | [[SpliceGrapher]] || 0.2.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Zcluster|Zcluster]] || [[File:Up20.png|20px|link=#top]]
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+| [[Sputnik]] || XX || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Zcluster|Zcluster]] || [[File:Up20.png|20px|link=#top]]
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 | [[SSAHA2]] || 2.5.5 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Zcluster|Zcluster]] || [[File:Up20.png|20px|link=#top]]

Software-old: Difference between revisions

Revision as of 08:15, 21 March 2013

Installed Software List

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