Software-old
Jump to navigation
Jump to search
Installed Software List
Last updated 2013-01-31.
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 | ||
BEAST | 1.7.2 | Bioinformatics | zcluster | ||
BEST Bayesian | 2.3.1 | Bioinformatics | zcluster | ||
BioPerl | 1.61 | Bioinformatics | zcluster | ||
BioPython | 1.58 | Bioinformatics | zcluster | ||
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 | ||
ClustalW | 2.1 | Bioinformatics | zcluster | ||
CONSEL | v0.20 | Bioinformatics | zcluster | ||
EMBOSS | 6.2.0 (updated at 04/17/2010) | Bioinformatics | zcluster | ||
FASTA | 36 | Bioinformatics | zcluster | ||
FIRE | 1.1 | Bioinformatics | zcluster | ||
FitModel | 0.5.3 | Bioinformatics | zcluster | ||
Genome | Phred version: 0.071220.c | Bioinformatics | zcluster | ||
Hmmer | 3.0 | Bioinformatics | zcluster | ||
IMa | May 06 | Bioinformatics | zcluster | ||
indel-Seq-Gen | 2.02 | Bioinformatics | zcluster | ||
iprscan (InterProScan) | 5.0 CR2 | Bioinformatics | zcluster | ||
MEME | 4.8.1 | Bioinformatics | zcluster | ||
Migrate | 3.0.3 | Bioinformatics | zcluster | ||
MrBayes | 3.1.2 | Bioinformatics | zcluster | ||
MUSCLE | 3.8.31 | Bioinformatics | zcluster | ||
PAML | Latest version 4.4 | Bioinformatics | zcluster | ||
Pfam_scan | 04282012 | Bioinformatics | zcluster | ||
pftools | 2.3.5 | Bioinformatics | zcluster | ||
PHYML | 20110919 | Bioinformatics | |||
RAxML | 04/26/2012 | Bioinformatics | zcluster | ||
Repeatmasker | 3.3 | Bioinformatics | zcluster | ||
RepeatScout | 1.05 | Bioinformatics | zcluster | ||
STEM | 2.0 | Bioinformatics | zcluster | ||
Tracer | v 1.5 | Bioinformatics | zcluster | ||
WISE2 | 2.2.0 | Bioinformatics | zcluster | ||
3D_DOCK | 2.0 | Computational Chemistry | pcluster | ||
AMBER- | 8 | Computational Chemistry | pcluster | ||
GAMESS | 2007 R6 | pcluster | |||
GAUSSIAN03 | 03 | Computational Chemistry | pcluster | ||
GAUSSIAN94 | 94 | Computational Chemistry | pcluster | ||
MOTECC qmdcp | 90 | Computational Chemistry | pcluster | ||
NWCHEM | 4.7 | Computational Chemistry | pcluster | ||
VMD | 1.8.4 | Computational Chemistry | zcluster | ||
Maple-pcluster | 10.06 | Other | pcluster | ||
Mathematica | 5.2 | Other | pcluster | ||
MatLab | R2012a (7.14.0.739) | Other | zcluster | ||
NETCDF | 3.5.1, 3.6.2 | Other | pcluster | ||
Sage | 3.1.1, 3.4.1 | Other | |||
R | 1.9.1, 2.1.1, 2.4.0 | pcluster | |||
R | 2.4.0, 2.5.1, 2.7.0 | zcluster | |||
SAS | 9.1 | Statistics | |||
Bl2seq | Bioinformatics | ||||
Blastall | Bioinformatics | zcluster | |||
BLASTCLUST | Bioinformatics | ||||
BLAST Databases | |||||
Blastpgp | Bioinformatics | ||||
fastacmd | |||||
Formatdb | |||||
MEGABLAST | |||||
Arabidopsis | Database | zcluster | |||
Arb | zcluster | ||||
Bacteria NCBI | zcluster | ||||
COG | zcluster | ||||
NCBI_database | Bioinformatics | zcluster | |||
gss | Bioinformatics | zcluster | |||
FISH | zcluster | ||||
Homo_sapien | zcluster | ||||
htgs | zcluster | ||||
KEGG | zcluster | ||||
Medicago | zcluster | ||||
Populus | zcluster | ||||
Refseq | zcluster | ||||
Rice TIGR | zcluster | ||||
Roseobacter | zcluster | ||||
Silva | zcluster | ||||
Sus_scrofa | zcluster | ||||
Uniprot | zcluster | ||||
Uniref | zcluster | ||||
WU Blast | 2.2.6 | Bioinformatics | zcluster | ||
AMBER | 8, 10 | Computational Chemistry | zcluster | ||
NAMD | 2.6b2, 2.7b1 | Computational Chemistry | pcluster | ||
NovoAlign | 2.07 | Bioinformatics | zcluster | ||
MAQ | 0.7.1 | Bioinformatics | zcluster | ||
MIRA | 3.9.9 | Bioinformatics | zcluster | ||
pebl | 1.01 | installed for Python 2.6.2 | |||
Burrows-Wheeler Aligner (BWA) | 0.6.2 | zcluster | |||
maize | Database | zcluster | |||
tophat | 2.0.5 | Bioinformatics | zcluster | ||
pfam | 26.0 | Database | zcluster | ||
ncbi blast parsers | Bioinformatics | zcluster | |||
Newbler | 2.6 | Bioinformatics | zcluster | ||
MOTHUR | 1.8.0, 1.9.0, 1.12.0 | zcluster | |||
velvet | 1.2.01 | Bioinformatics | zcluster | ||
bowtie | 0.12.8 | Bioinformatics | zcluster | ||
Qiime | 1.3.0 | Bioinformatics | zcluster | ||
QTL Cartographer | 1.17j | Bioinformatics | zcluster | ||
ViennaRNA | 1.8.5 | Bioinformatics | zcluster | ||
RNAz | 2.1 | Bioinformatics | zcluster | ||
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 | ||
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 | ||
NCBI Blast + | 2.2.26 is the last updated | Bioinformatics | zcluster | ||
LASTZ | 1.03.02 | Bioinformatics | zcluster | ||
samtools | 0.1.18 | Bioinformatics | zcluster | ||
git | 1.7.4.1, 1.7.9 | Others | |||
BS Seeker | download at Dec 113 | Bioinformatics | |||
mafft | 6.864b | Bioinformatics | zcluster | ||
opal | 2.0.0 | Bioinformatics | zcluster | ||
SATé | 2.2.4 | Bioinformatics | zcluster | ||
MOTECC qmdcp | 90 | Computational Chemistry | zcluster | ||
Ray | 1.4.0, 1.6.1-0 | Bioinformatics | |||
Trinity | Versions r2012-10-05 | Bioinformatics | zcluster | ||
k-link | 03 27, 2009 | Bioinformatics | |||
FastX | Version 0.0.13, 0.0.13.2 | Bioinformatics | |||
MyScanACE | 04232012 | Bioinformatics | zcluster | ||
gatk | 2.2-2-gf44cc4e | Bioinformatics | zcluster | ||
breakdancer | 1.1_2011_02_21 | Bioinformatics | zcluster | ||
CREST | 1.0 | Bioinformatics | zcluster | ||
SOAPdenovo | 1.05 | Bioinformatics | zcluster | ||
SEQuel | 1.0.2 | Bioinformatics | zcluster | ||
cd-hit | 4.5.6 | Bioinformatics | zcluster | ||
amos | 3.1.0 | Bioinformatics | zcluster | ||
lsa | 11182011 | Bioinformatics | zcluster | ||
mrfast | 2.5.0.4 | Bioinformatics | zcluster | ||
tassel | 4.0 | Bioinformatics | zcluster | ||
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 | zcluster | ||
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 | zcluster | ||
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 | Other | 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 | Other | 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 | ||
AMBER | 11, 12 | Computational Chemistry | zcluster | ||
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 | zcluster | ||
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 |