Software-old: Difference between revisions

Revision as of 08:52, 24 September 2013

Installed Software List

Last updated 2013-09-24.

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

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	1.3.6	Bioinformatics	Zcluster
ACT	03/27/2013	Bioinformatics	Zcluster
ADMIXTOOLS	1.1	Bioinformatics	Zcluster
Admixture	1.22	Bioinformatics	Zcluster
AFNI	2013.04.26	Other	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	0.7.0	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	0.12.9	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)	0.7.4	Bioinformatics	Zcluster
bx-python	06/24/2013	Bioinformatics	Zcluster
cap3	10/2011	Bioinformatics	Zcluster
casava	1.8.2	Bioinformatics	Zcluster
cd-hit	4.6.1	Bioinformatics	Zcluster
cdbfasta	04282012	Bioinformatics	Zcluster
cdbtools	06172013	Bioinformatics	Zcluster
CEAS	1.0.2	Bioinformatics	Zcluster
CEGMA	2.4.010312	Bioinformatics	Zcluster
CFOUR	beta	Chemistry	Zcluster
circoletto	05.10.12	Bioinformatics	Zcluster
circos	0.64	Bioinformatics	Zcluster
CLAPACK	3.2.1	Math Library	Zcluster
CLUMPP	1.1.2	Bioinformatics	Zcluster
ClustalW	2.1	Bioinformatics	Zcluster
CNVnator	0.2.7	Bioinformatics	Zcluster
cnv-seq	0.2-7	Bioinformatics	Zcluster
Coding Potential Calculator	0.9-r2	Bioinformatics	Zcluster
Conclustador	0.4a	Bioinformatics	Zcluster
Consed	26.0	Bioinformatics	Zcluster
CONSEL	v0.20	Bioinformatics	Zcluster
CORMA	5.21	Chemistry	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	2.1.1	Bioinformatics	Zcluster
cutadapt	1.2.1	Bioinformatics	Zcluster
CWEB	3.64	Other	Zcluster
DeconSeq	0.4.2	Bioinformatics	Zcluster
demuxipy	1.0	Bioinformatics	Zcluster
ddRADseq	0.01	Bioinformatics	Zcluster
DLCoal	1.0	Bioinformatics	Zcluster
dnasam	20100621	Bioinformatics	Zcluster
drmma	0.5	Other	Zcluster
ea-utils	1.1.2-537	Bioinformatics	Zcluster
edena	v3.130110	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	0.0.13.2	Bioinformatics	Zcluster
FCP	1.0.4	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
F-Seq	1.84	Bioinformatics	Zcluster
Fsl	5.0.4	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
garli	2.01	Bioinformatics	Zcluster
gatk	2.5-2-gf57256b	Bioinformatics	Zcluster
GAUSSIAN03	03	Chemistry	Pcluster
GAUSSIAN94	94	Chemistry	Pcluster
Gblocks	0.91b	Bioinformatics	Zcluster
GDB	7.0.1	Debugger	Zcluster
GEM	3rd pre-release	Bioinformatics	Zcluster
GeneMark	genemark-ES 2.3e gGeneMark version 2.5m	Bioinformatics	Zcluster
Genome	Phred version: 0.071220.c	Bioinformatics	Zcluster
GenomeMapper	0.4.4 (Version for SHORE/WMD3)	Bioinformatics	Zcluster
GenomeTools	1.5.1	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-gsnap	2013-09-11	Bioinformatics	Zcluster
GNU Compilers	4.1.2, 4.4.6, 4.5.3, 4.7.1	Compiler	Zcluster
GNUMAP	3.0.2	Bioinformatics	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, 4.6.1	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	3.1	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
IGVTools	2.3.14	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 RC7	Bioinformatics	Zcluster
iscan	1.0.0	Bioinformatics	Zcluster
JAGS	3.3.0	Statistics	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
KmerGenie	1.5393	Bioinformatics	Zcluster
LAPACK	3.0, 3.4.2	Math Library	Zcluster
LASTZ	1.03.02	Bioinformatics	Zcluster
LCS	0.2.4	Bioinformatics	Zcluster
LDDist	1.3.2	Bioinformatics	Zcluster
libsequence	1.7.4	Bioinformatics	Zcluster
LIBSVM	3.17	Other	Zcluster
LLVM-Clang	3.1	Compiler	Zcluster
lsa	11182011	Bioinformatics	Zcluster
macs	1.4.2	Bioinformatics	Zcluster
Mafft	7.029-e	Bioinformatics	Zcluster
maker	2.10	Bioinformatics	Zcluster
Maple	16	Other, Programming, Graphics	Zcluster
Maple-pcluster	10.06	Other, Programming, Graphics	Pcluster
MapSplice2	2.1.5	Other, Programming, Graphics	Zcluster
MAQ	0.7.1	Bioinformatics	Zcluster
MARDIGRAS	3.21	Chemistry	Zcluster
Mathematica	9.0	Other, Programming , Graphics	Zcluster
Mathematica-pcluster	5.2	Other, Programming , Graphics	Pcluster
MatLab	R2012a (7.14.0.739)	Other, Programming, Graphics	Zcluster
Mauve	2.3.1	Bioinformatics	Zcluster
MCL	12-135	Bioinformatics	Zcluster
MEAD	2.2.9	Chemistry	Zcluster
megan	4.67.2	Bioinformatics	Zcluster
MEME	4.8.1	Bioinformatics	Zcluster
METIS	4.0.3, 5.1.0	Math Library	Zcluster
Migrate	3.5.1	Bioinformatics	Zcluster
Minia	1.4683	Bioinformatics	Zcluster
MIRA	3.9.9	Bioinformatics	Zcluster
MITE-Hunter	11-2011	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
MOTHUR	1.30.0	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
MUMPS	4.10.0	Math Library	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 +	2.2.28	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
netCDF4-python	1.0.5	Library	Zcluster
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
nseg	04182013	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, 2.4.4	Other	Zcluster
opera	1.3.1	Bioinformatics	Zcluster
OrthoMCL	2.0.3	Bioinformatics	Zcluster
OSPREY	2.0	Bioinformatics	Zcluster
p4	r231	Bioinformatics	Zcluster
PacBioToCA	7.0	Bioinformatics	Zcluster
pagan	0.39	Bioinformatics	Zcluster
pagit	v1	Bioinformatics	Zcluster
PAML	4.4	Bioinformatics	Zcluster
pandaseq	2.0	Bioinformatics	Zcluster
Papara_nt	2.1.2	Bioinformatics	Zcluster
ParMETIS	3.2.0, 4.0.3	Math Library	Zcluster
ParseRNAseq	1.0	Bioinformatics	Zcluster
PASA	r20130605p1	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
PETSc	3.1-p8, 3.4.2	Math Library	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, 1.4e	Bioinformatics	Zcluster
Phylip	3.69	Bioinformatics	Zcluster
PHYML	20110919	Bioinformatics	Zcluster
picard	1.87	Bioinformatics	Zcluster
pileup	0.6	Bioinformatics	Zcluster
pindel	0.2.4t	Bioinformatics	Zcluster
pknotsRG	1.3	Bioinformatics	Zcluster
plink	1.07	Bioinformatics	Zcluster
prank	100802	Bioinformatics	Zcluster
Primer3	2.3.4	Bioinformatics	Zcluster
Prokka	1.6	Bioinformatics	Zcluster
Prottest3	3.2.1	Bioinformatics	Zcluster
psmc	0.6.4-r33	Bioinformatics	Zcluster
PRINSEQ	0.20.3	Bioinformatics	Zcluster
pynast	1.2	Bioinformatics	Zcluster
pysam	0.6	Bioinformatics	Zcluster
PyTables	2.3.1	Other	Zcluster
PyNIO	1.4.1	Other	Zcluster
Python	2.4.3, 2.7.2, 3.3.0	Programming	Zcluster
Qiime	1.7.0	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, 3.0.0	Statistics	Zcluster
R-pcluster	1.9.1, 2.1.1	Statistics	Pcluster
RADnome	0.0.1-7-25	Bioinformatics	Zcluster
RAxML	04/26/2012	Bioinformatics	Zcluster
RAxML-Light	1.0.5	Bioinformatics	Zcluster
RAPSearch2	2.12	Bioinformatics	Zcluster
RCCBatchBlast	5.0	Bioinformatics	Zcluster
RCCBatchBlastPlus	1.0	Bioinformatics	Zcluster
RECON	1.05	Bioinformatics	Zcluster
Repeatmasker	4.0.1	Bioinformatics	Zcluster
Repeatmodeler	1.0.7	Bioinformatics	Zcluster
Reptile	1.1	Bioinformatics	Zcluster
RepeatScout	1.05	Bioinformatics	Zcluster
RESG	0.4.8	Bioinformatics	Zcluster
riboPicker	0.4.3	Bioinformatics	Zcluster
RIP	4	Other	Zcluster
RITA	1.0.1	Bioinformatics	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
RogueNaRok	1.0	Bioinformatics	Zcluster
ROOT	5.34.09	Library	Zcluster
RSAT (RSA-tools)	1.0	Bioinformatics	Zcluster
RSEM	1.2.7	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
ScaLAPACK	2.0.2	Math Library	Zcluster
SEAStAR	0.4.8	Bioinformatics	Zcluster
SEQuel	1.0.2	Bioinformatics	Zcluster
seqtk	07052013	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
SNAPP	1.1.1	Bioinformatics	Zcluster
snow	0.3-8, 0.3-10, 0.3-12	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
Splitaake	1.0	Bioinformatics	Zcluster
spolpred	09/10/2013	Bioinformatics	Zcluster
Sputnik	03/20/2013	Bioinformatics	Zcluster
SRA	2.1.9	Bioinformatics	Zcluster
SSAHA2	2.5.5	Bioinformatics	Zcluster
SSAKE	v3-8	Bioinformatics	Zcluster
SSPACE	2.0	Bioinformatics	Zcluster
stacks	1.06	Bioinformatics	Zcluster
STAMPY	1.0.21	Bioinformatics	Zcluster
STEM	2.0	Bioinformatics	Zcluster
strauto	0.3.1	Bioinformatics	Zcluster
structure	2.3.4	Bioinformatics	Zcluster
structurama	2.0	Bioinformatics	Zcluster
SuperLU	4.3	Math Library	Zcluster
SuperLU_dist	3.3	Math Library	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
TagCleaner	0.13	Bioinformatics	Zcluster
TAPDANCE	03/20/2013	Bioinformatics	Zcluster
tassel	4.0	Bioinformatics	Zcluster
tax2tree	1.0	Bioinformatics	Zcluster
tgicl	2.1	Bioinformatics	Zcluster
TIGER	1.02	Bioinformatics	Zcluster
tophat	2.0.9	Bioinformatics	Zcluster
trans-abyss	1.4.4	Bioinformatics	Zcluster
Tracer	v 1.5	Bioinformatics	Zcluster
treemix	1.12	Bioinformatics	Zcluster
trimmomatic	0.27	Bioinformatics	Zcluster
Trinity	r2013_08_14	Bioinformatics	Zcluster
UClust	1.2.22q	Bioinformatics	Zcluster
UNAFold	3.8	Bioinformatics	Zcluster
UPP	2.0	Other	Zcluster
usearch	v6.0.30	Bioinformatics	Zcluster
vcftools	0.1.11	Bioinformatics	Zcluster
velvet	1.2.01	Bioinformatics	Zcluster
VelvetOptimiser	2.2.5	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
wgs	7.0	Bioinformatics	Zcluster
wigToBigWig	v4	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
Zorro	2.2	Bioinformatics	Zcluster

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@@ Line 696: / Line 696: @@
 | [[TIGER]] || 1.02 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Zcluster|Zcluster]] || [[File:Up20.png|20px|link=#top]]
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-| [[tophat]] || 2.0.5 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Zcluster|Zcluster]] || [[File:Up20.png|20px|link=#top]]
+| [[tophat]] || 2.0.9 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Zcluster|Zcluster]] || [[File:Up20.png|20px|link=#top]]
 |-
 | [[trans-abyss]] || 1.4.4 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Zcluster|Zcluster]] || [[File:Up20.png|20px|link=#top]]

Software-old: Difference between revisions

Revision as of 08:52, 24 September 2013

Installed Software List

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