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! scope="col" width="60px"| Cluster | ! scope="col" width="60px"| Cluster | ||
! scope="col" | Notes | ! scope="col" | Notes | ||
! scope="col" | Reviewed By | |||
|- | |- | ||
| [[00-Skipped Page]] || 0.0 || Work Log || GACRC || YH Created | | [[00-Skipped Page]] || 0.0 || Work Log || GACRC || YH Created || | ||
|- | |- | ||
| [[3D_DOCK]] || 2.0 || Chemistry || pcluster || Ignored by SMW, YH reviewed, need SHT review | | [[3D_DOCK]] || 2.0 || Chemistry || pcluster || Ignored by SMW, || YH reviewed, need SHT review | ||
|- | |- | ||
| [[454 Software]] || || Bioinformatics || zcluster || Done, SMW | | [[454 Software]] || || Bioinformatics || zcluster || Done, SMW || | ||
|- | |- | ||
| [[aaarf]] || 1.0.0 || Bioinformatics || zcluster || Done, SMW | | [[aaarf]] || 1.0.0 || Bioinformatics || zcluster || Done, SMW || | ||
|- | |- | ||
| [[ABINIT]] || 6.12.1 || Chemistry || zcluster || Done, SMW | | [[ABINIT]] || 6.12.1 || Chemistry || zcluster || Done, SMW || | ||
|- | |- | ||
| [[ABySS]] || 1.3.4 || Bioinformatics || zcluster || Done, SMW | | [[ABySS]] || 1.3.4 || Bioinformatics || zcluster || Done, SMW || | ||
|- | |- | ||
| [[ALLPATHS-LG]] || 44254 || Bioinformatics || zcluster || Contains Dead Links, SMW | | [[ALLPATHS-LG]] || 44254 || Bioinformatics || zcluster || Contains Dead Links, SMW || | ||
|- | |- | ||
| [[AMBER]] || 11, 12 || Chemistry || zcluster || Done, SHT | | [[AMBER]] || 11, 12 || Chemistry || zcluster || Done, SHT || | ||
|- | |- | ||
| [[AMBER-pcluster]] || 8 || Chemistry || pcluster || | | [[AMBER-pcluster]] || 8 || Chemistry || pcluster || || | ||
|- | |- | ||
| [[amos]] || 3.1.0 || Bioinformatics || zcluster || Done, SMW | | [[amos]] || 3.1.0 || Bioinformatics || zcluster || Done, SMW || | ||
|- | |- | ||
| [[Arabidopsis]] || || Database || zcluster || | | [[Arabidopsis]] || || Database || zcluster || || | ||
|- | |- | ||
| [[ARB]] || 5.3 || Bioinformatics || zcluster || ?, Please Review Running Program Section, SMW | | [[ARB]] || 5.3 || Bioinformatics || zcluster || ?, Please Review Running Program Section, SMW || Done, YH reviewed | ||
|- | |- | ||
| [[Arb]] || || Database || zcluster || | | [[Arb]] || || Database || zcluster || || | ||
|- | |- | ||
| [[AUGUSTUS]] || 2.5.5 || Bioinformatics || zcluster || Please verify Documentation Section, SMW | | [[AUGUSTUS]] || 2.5.5 || Bioinformatics || zcluster || Please verify Documentation Section, SMW || | ||
|- | |- | ||
| [[Bacteria NCBI]] || || Database || zcluster || | | [[Bacteria NCBI]] || || Database || zcluster || || | ||
|- | |- | ||
| [[bam2fastq]] || 1.1.0 || Bioinformatics || zcluster || Done, SMW | | [[bam2fastq]] || 1.1.0 || Bioinformatics || zcluster || Done, SMW || | ||
|- | |- | ||
| [[BEAST]] || 1.7.2 || Bioinformatics || zcluster || Done, with Dead Links, SMW | | [[BEAST]] || 1.7.2 || Bioinformatics || zcluster || Done, with Dead Links, SMW || | ||
|- | |- | ||
| [[BEDTools]] || 2.16.2 || Bioinformatics || zcluster || | | [[BEDTools]] || 2.16.2 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[BEST Bayesian]] || 2.3.1 || Bioinformatics || zcluster || | | [[BEST Bayesian]] || 2.3.1 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[BioPerl]] || 1.61 || Bioinformatics || zcluster || | | [[BioPerl]] || 1.61 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[BioPython]] || 1.58 || Bioinformatics || zcluster || | | [[BioPython]] || 1.58 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[Bismark Bisulfite Mapper]] || 0.7.6 || Bioinformatics || zcluster || | | [[Bismark Bisulfite Mapper]] || 0.7.6 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[BiSS]] || 0.0.1 || Bioinformatics || zcluster || | | [[BiSS]] || 0.0.1 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[Bl2seq]] || || Bioinformatics || zcluster || | | [[Bl2seq]] || || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[BLAST Databases]] || || Database || zcluster || | | [[BLAST Databases]] || || Database || zcluster || || | ||
|- | |- | ||
| [[Blastall]] || || Bioinformatics || zcluster || | | [[Blastall]] || || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[BLASTCLUST]] || || Bioinformatics || zcluster || | | [[BLASTCLUST]] || || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[Blastpgp]] || || Bioinformatics || zcluster || | | [[Blastpgp]] || || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[Blat]] || 3.5 || Bioinformatics || zcluster || | | [[Blat]] || 3.5 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[BMGE]] || 1.1 || Bioinformatics || zcluster || | | [[BMGE]] || 1.1 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[bowtie]] || 0.12.8 || Bioinformatics || zcluster || | | [[bowtie]] || 0.12.8 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[bowtie2]] || 2.0.0-beta7 || Bioinformatics || zcluster || | | [[bowtie2]] || 2.0.0-beta7 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[breakdancer]] || 1.1_2011_02_21 || Bioinformatics || zcluster || | | [[breakdancer]] || 1.1_2011_02_21 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[brownie]] || 2.1.2 || Bioinformatics || zcluster || | | [[brownie]] || 2.1.2 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[BS Seeker]] || Dec 113 || Bioinformatics || zcluster || | | [[BS Seeker]] || Dec 113 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[Burrows-Wheeler Aligner (BWA)]] || 0.6.2 || Bioinformatics || zcluster || | | [[Burrows-Wheeler Aligner (BWA)]] || 0.6.2 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[cd-hit]] || 4.5.6 || Bioinformatics || zcluster || | | [[cd-hit]] || 4.5.6 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[cdbfasta]] || 04282012 || Bioinformatics || zcluster || | | [[cdbfasta]] || 04282012 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[CEAS]] || 1.0.2 || Bioinformatics || zcluster || | | [[CEAS]] || 1.0.2 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[CEGMA]] || 2.4.010312 || Bioinformatics || zcluster || | | [[CEGMA]] || 2.4.010312 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[circos]] || 0.62 || Bioinformatics || zcluster || | | [[circos]] || 0.62 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[ClustalW]] || 2.1 || Bioinformatics || zcluster || | | [[ClustalW]] || 2.1 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[Coding Potential Calculator]] || 0.9-r2 || Bioinformatics || zcluster || | | [[Coding Potential Calculator]] || 0.9-r2 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[COG]] || || || zcluster || | | [[COG]] || || || zcluster || || | ||
|- | |- | ||
| [[CONSEL]] || v0.20 || Bioinformatics || zcluster || | | [[CONSEL]] || v0.20 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[cortex_con]] || 0.04c || Bioinformatics || zcluster || | | [[cortex_con]] || 0.04c || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[cortex_var]] || 1.0.5.3 || Bioinformatics || zcluster || | | [[cortex_var]] || 1.0.5.3 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[Count]] || 2010-04-02 || Bioinformatics || zcluster || | | [[Count]] || 2010-04-02 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[CREST]] || 1.0 || Bioinformatics || zcluster || | | [[CREST]] || 1.0 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[ctrax]] || 0.3.2 || Other || zcluster || | | [[ctrax]] || 0.3.2 || Other || zcluster || || | ||
|- | |- | ||
| [[cufflinks]] || 2.0.2 || Bioinformatics || zcluster || | | [[cufflinks]] || 2.0.2 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[cutadapt]] || 1.1 || Bioinformatics || zcluster || | | [[cutadapt]] || 1.1 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[ddRADseq]] || || Bioinformatics || zcluster || | | [[ddRADseq]] || || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[DLCoal]] || 1.0 || Bioinformatics || zcluster || | | [[DLCoal]] || 1.0 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[drmma]] || 0.5 || Other || zcluster || | | [[drmma]] || 0.5 || Other || zcluster || || | ||
|- | |- | ||
| [[ea-utils]] || 1.1.2-537 || Bioinformatics || zcluster || | | [[ea-utils]] || 1.1.2-537 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[edena]] || 3Dev120626 || Bioinformatics || zcluster || | | [[edena]] || 3Dev120626 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[EMBOSS]] || 6.2.0 || Bioinformatics || zcluster || | | [[EMBOSS]] || 6.2.0 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[emmix]] || 1.3 || Bioinformatics || zcluster || | | [[emmix]] || 1.3 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[ESTscan]] || 3.0.3 || Bioinformatics || zcluster || Done, YH | | [[ESTscan]] || 3.0.3 || Bioinformatics || zcluster || Done, YH || | ||
|- | |- | ||
| [[evm (EVidenceModeler)]] || r2012-06-25 || Bioinformatics || zcluster || | | [[evm (EVidenceModeler)]] || r2012-06-25 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[ExaML]] || 315576 || Bioinformatics || zcluster || | | [[ExaML]] || 315576 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[exonerate]] || 2.2.0 || Bioinformatics || zcluster || | | [[exonerate]] || 2.2.0 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[FAR]] || 2.15 || Bioinformatics || zcluster || | | [[FAR]] || 2.15 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[FASTA]] || 36 || Bioinformatics || zcluster || | | [[FASTA]] || 36 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[FastQC]] || 0.10.1 || Bioinformatics || zcluster || | | [[FastQC]] || 0.10.1 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[fasttree]] || 2.1.4 || Bioinformatics || zcluster || | | [[fasttree]] || 2.1.4 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[FastX]] || 0.0.13, 0.0.13.2 || Bioinformatics || zcluster || | | [[FastX]] || 0.0.13, 0.0.13.2 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[FIRE]] || 1.1 || Bioinformatics || zcluster || | | [[FIRE]] || 1.1 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[FISH]] || || Database || zcluster || | | [[FISH]] || || Database || zcluster || || | ||
|- | |- | ||
| [[FitModel]] || 0.5.3 || Bioinformatics || zcluster || | | [[FitModel]] || 0.5.3 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[FLASH]] || 1.0.3 || Bioinformatics || zcluster || | | [[FLASH]] || 1.0.3 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[GAMESS]] || May2012R1 with XMVB 2.0. || Chemistry || zcluster || | | [[GAMESS]] || May2012R1 with XMVB 2.0. || Chemistry || zcluster || || | ||
|- | |- | ||
| [[GAMESS-pcluster]] || 2007 R6 || Chemistry || pcluster || | | [[GAMESS-pcluster]] || 2007 R6 || Chemistry || pcluster || || | ||
|- | |- | ||
| [[GapFiller]] || 1.11 || Bioinformatics || zcluster || | | [[GapFiller]] || 1.11 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[gatk]] || 2.2-2-gf44cc4e || Bioinformatics || zcluster || | | [[gatk]] || 2.2-2-gf44cc4e || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[GAUSSIAN03]] || 03 || Chemistry || pcluster || | | [[GAUSSIAN03]] || 03 || Chemistry || pcluster || || | ||
|- | |- | ||
| [[GAUSSIAN94]] || 94 || Chemistry || pcluster || | | [[GAUSSIAN94]] || 94 || Chemistry || pcluster || || | ||
|- | |- | ||
| [[Gblocks]] || 0.91b || Bioinformatics || zcluster || | | [[Gblocks]] || 0.91b || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[GeneMark]] || genemark-ES 2.3e gGeneMark version 2.5m || Bioinformatics || zcluster || | | [[GeneMark]] || genemark-ES 2.3e gGeneMark version 2.5m || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[Genome]] || Phred version: 0.071220.c || Bioinformatics || zcluster || | | [[Genome]] || Phred version: 0.071220.c || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[GenomeMapper]] || 0.4.3 (Version for SHORE/WMD3) || Bioinformatics || zcluster || | | [[GenomeMapper]] || 0.4.3 (Version for SHORE/WMD3) || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[GenomeTools]] || 1.3.9 || Bioinformatics || zcluster || | | [[GenomeTools]] || 1.3.9 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[git]] || 1.7.4.1, 1.7.9 || Others || zcluster || | | [[git]] || 1.7.4.1, 1.7.9 || Others || zcluster || || | ||
|- | |- | ||
| [[Glimmer]] || 3.0.2 || Bioinformatics || zcluster || | | [[Glimmer]] || 3.0.2 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[GlimmerHMM]] || 3.0.1 || Bioinformatics || zcluster || | | [[GlimmerHMM]] || 3.0.1 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[gmap]] || 2007-09-28 || Bioinformatics || zcluster || | | [[gmap]] || 2007-09-28 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[gmap-gsnap]] || 2012-07-20 || Bioinformatics || zcluster || | | [[gmap-gsnap]] || 2012-07-20 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[gnuplot]] || 4.0, 4.6.0 || Graphics || zcluster || Done, SHT | | [[gnuplot]] || 4.0, 4.6.0 || Graphics || zcluster || Done, SHT || | ||
|- | |- | ||
| [[gpu-blast]] || 1.1 with ncbi-blast-2.2.25+ || Bioinformatics || zcluster || | | [[gpu-blast]] || 1.1 with ncbi-blast-2.2.25+ || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[grace]] || 5.1.22 || Other || zcluster || | | [[grace]] || 5.1.22 || Other || zcluster || || | ||
|- | |- | ||
| [[Gromacs]] || 4.5.5 || Chemistry || zcluster || Done, SHT | | [[Gromacs]] || 4.5.5 || Chemistry || zcluster || Done, SHT || | ||
|- | |- | ||
| [[gss]] || || Bioinformatics || zcluster || | | [[gss]] || || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[HDF5]] || 1.6.4, 1.8.9 || Other || zcluster || | | [[HDF5]] || 1.6.4, 1.8.9 || Other || zcluster || || | ||
|- | |- | ||
| [[Hmmer]] || 3.0 || Bioinformatics || zcluster || | | [[Hmmer]] || 3.0 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[Homo_sapien]] || || Database || zcluster || | | [[Homo_sapien]] || || Database || zcluster || || | ||
|- | |- | ||
| [[htgs]] || || Database || zcluster || | | [[htgs]] || || Database || zcluster || || | ||
|- | |- | ||
| [[htseq]] || 0.5.3p3 || Bioinformatics || zcluster || | | [[htseq]] || 0.5.3p3 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[igb]] || 6.7.3 || Bioinformatics || zcluster || | | [[igb]] || 6.7.3 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[IGV]] || 2.1.23 || Bioinformatics || zcluster || | | [[IGV]] || 2.1.23 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[IMa]] || May 06 || Bioinformatics || zcluster || | | [[IMa]] || May 06 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[indel-Seq-Gen]] || 2.02 || Bioinformatics || zcluster || | | [[indel-Seq-Gen]] || 2.02 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[InStruct]] || 3.2.09 || Bioinformatics || zcluster || | | [[InStruct]] || 3.2.09 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[iprscan (InterProScan)]] || 5.0 CR2 || Bioinformatics || zcluster || | | [[iprscan (InterProScan)]] || 5.0 CR2 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[iscan]] || 1.0.0 || Bioinformatics || zcluster || | | [[iscan]] || 1.0.0 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[Jellyfish]] || 1.1.5 || Bioinformatics || zcluster || | | [[Jellyfish]] || 1.1.5 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[k-link]] || 03 27, 2009 || Bioinformatics || zcluster || | | [[k-link]] || 03 27, 2009 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[KEGG]] || || Database || zcluster || | | [[KEGG]] || || Database || zcluster || || | ||
|- | |- | ||
| [[LASTZ]] || 1.03.02 || Bioinformatics || zcluster || | | [[LASTZ]] || 1.03.02 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[LDDist]] || 1.3.2 || Bioinformatics || zcluster || | | [[LDDist]] || 1.3.2 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[libsequence]] || 1.7.4 || Bioinformatics || zcluster || | | [[libsequence]] || 1.7.4 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[LLVM-Clang]] || 3.1 || Compiler || zcluster || | | [[LLVM-Clang]] || 3.1 || Compiler || zcluster || || | ||
|- | |- | ||
| [[lsa]] || 11182011 || Bioinformatics || zcluster || | | [[lsa]] || 11182011 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[macs]] || 1.4.2 || Bioinformatics || zcluster || | | [[macs]] || 1.4.2 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[mafft]] || 6.864b || Bioinformatics || zcluster || | | [[mafft]] || 6.864b || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[maize]] || || Database || zcluster || | | [[maize]] || || Database || zcluster || || | ||
|- | |- | ||
| [[maker]] || 2.10 || Bioinformatics || zcluster || | | [[maker]] || 2.10 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[Maple-pcluster]] || 10.06 || Other || pcluster || | | [[Maple-pcluster]] || 10.06 || Other || pcluster || || | ||
|- | |- | ||
| [[MAQ]] || 0.7.1 || Bioinformatics || zcluster || | | [[MAQ]] || 0.7.1 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[Mathematica]] || 5.2 || Other || pcluster || | | [[Mathematica]] || 5.2 || Other || pcluster || || | ||
|- | |- | ||
| [[MatLab]] || R2012a (7.14.0.739) || Other || zcluster || | | [[MatLab]] || R2012a (7.14.0.739) || Other || zcluster || || | ||
|- | |- | ||
| [[MCL]] || 12-135 || Bioinformatics || zcluster || | | [[MCL]] || 12-135 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[MEAD]] || 2.2.9 || Chemistry || zcluster || | | [[MEAD]] || 2.2.9 || Chemistry || zcluster || || | ||
|- | |- | ||
| [[Medicago]] || || Database || zcluster || | | [[Medicago]] || || Database || zcluster || || | ||
|- | |- | ||
| [[megan]] || 4.67.2 || Bioinformatics || zcluster || | | [[megan]] || 4.67.2 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[MEME]] || 4.8.1 || Bioinformatics || zcluster || | | [[MEME]] || 4.8.1 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[Migrate]] || 3.0.3 || Bioinformatics || zcluster || | | [[Migrate]] || 3.0.3 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[Minia]] || 1.4683 || Bioinformatics || zcluster || | | [[Minia]] || 1.4683 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[MIRA]] || 3.9.9 || Bioinformatics || zcluster || | | [[MIRA]] || 3.9.9 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[MOTECC qmdcp]] || 90 || Chemistry || zcluster || | | [[MOTECC qmdcp]] || 90 || Chemistry || zcluster || || | ||
|- | |- | ||
| [[MOTECC qmdcp pcluster ]] || 90 || Chemistry || pcluster || | | [[MOTECC qmdcp pcluster ]] || 90 || Chemistry || pcluster || || | ||
|- | |- | ||
| [[MOTHUR]] || 1.28.0 || Bioinformatics || zcluster || | | [[MOTHUR]] || 1.28.0 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[mpi4py]] || 1.3 || Utilities || zcluster || | | [[mpi4py]] || 1.3 || Utilities || zcluster || || | ||
|- | |- | ||
| [[mpiblast]] || 1.6.0 || Bioinformatics || zcluster || | | [[mpiblast]] || 1.6.0 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[MrBayes]] || 3.1.2 || Bioinformatics || zcluster || | | [[MrBayes]] || 3.1.2 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[mrfast]] || 2.5.0.4 || Bioinformatics || zcluster || | | [[mrfast]] || 2.5.0.4 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[MSA]] || 3.8.1b || Bioinformatics || zcluster || | | [[MSA]] || 3.8.1b || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[MUSCLE]] || 3.8.31 || Bioinformatics || zcluster || | | [[MUSCLE]] || 3.8.31 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[MyScanACE]] || 04232012 || Bioinformatics || zcluster || | | [[MyScanACE]] || 04232012 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[NAMD]] || 2.9 || Chemistry || zcluster || | | [[NAMD]] || 2.9 || Chemistry || zcluster || || | ||
|- | |- | ||
| [[NAMD-pcluster]] || 2.6b2, 2.7b1 || Chemistry || pcluster || | | [[NAMD-pcluster]] || 2.6b2, 2.7b1 || Chemistry || pcluster || || | ||
|- | |- | ||
| [[NCBI Blast]] || 2.2.26 || Bioinformatics || zcluster || Done, | | [[NCBI Blast]] || 2.2.26 || Bioinformatics || zcluster || Done, YH || | ||
|- | |- | ||
| [[NCBI Blast +]] || 2.2.26 || Bioinformatics || zcluster || | | [[NCBI Blast +]] || 2.2.26 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[ncbi blast parsers]] || || Bioinformatics || zcluster || | | [[ncbi blast parsers]] || || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[NCBI_database]] || || Bioinformatics || zcluster || | | [[NCBI_database]] || || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[NETCDF]] || 4.1.3 || Other || zcluster || | | [[NETCDF]] || 4.1.3 || Other || zcluster || || | ||
|- | |- | ||
| [[NETCDF-pcluster]] || 3.5.1, 3.6.2 || Other || pcluster || | | [[NETCDF-pcluster]] || 3.5.1, 3.6.2 || Other || pcluster || || | ||
|- | |- | ||
| [[netlogo]] || 5.0 || Other || zcluster || | | [[netlogo]] || 5.0 || Other || zcluster || || | ||
|- | |- | ||
| [[Newbler]] || 2.6 || Bioinformatics || zcluster || | | [[Newbler]] || 2.6 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[NH PhyloBayes]] || 0.2.3 || Bioinformatics || zcluster || | | [[NH PhyloBayes]] || 0.2.3 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[nhPhyML]] || 01/2012 || Bioinformatics || zcluster || | | [[nhPhyML]] || 01/2012 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[NovelSeq]] || 1.0.2 || Bioinformatics || zcluster || | | [[NovelSeq]] || 1.0.2 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[NovoAlign]] || 2.07 || Bioinformatics || zcluster || | | [[NovoAlign]] || 2.07 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[numexp]] || 1.4.2 || Other || zcluster || | | [[numexp]] || 1.4.2 || Other || zcluster || || | ||
|- | |- | ||
| [[NWCHEM]] || 4.7 || Chemistry || pcluster || | | [[NWCHEM]] || 4.7 || Chemistry || pcluster || || | ||
|- | |- | ||
| [[opal]] || 2.0.0 || Bioinformatics || zcluster || | | [[opal]] || 2.0.0 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[Open Babel]] || 2.3.1 || Chemistry || zcluster || | | [[Open Babel]] || 2.3.1 || Chemistry || zcluster || || | ||
|- | |- | ||
| [[OpenBUGS]] || 3.2.2 || Statistics || zcluster || | | [[OpenBUGS]] || 3.2.2 || Statistics || zcluster || || | ||
|- | |- | ||
| [[OpenCV]] || 2.3.1 || Other || zcluster || | | [[OpenCV]] || 2.3.1 || Other || zcluster || || | ||
|- | |- | ||
| [[OSPREY]] || 2.0 || Bioinformatics || zcluster || | | [[OSPREY]] || 2.0 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[p4]] || r231 || Bioinformatics || zcluster || | | [[p4]] || r231 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[pagan]] || 0.39 || Bioinformatics || zcluster || | | [[pagan]] || 0.39 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[PAML]] || 4.4 || Bioinformatics || zcluster || | | [[PAML]] || 4.4 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[pandaseq]] || 2.0 || Bioinformatics || zcluster || | | [[pandaseq]] || 2.0 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[Papara_nt]] || 2.1.2 || Bioinformatics || zcluster || | | [[Papara_nt]] || 2.1.2 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[PASHA]] || 1.0.6 || Bioinformatics || zcluster || | | [[PASHA]] || 1.0.6 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[PeakSplitter]] || 1.0 || Bioinformatics || zcluster || | | [[PeakSplitter]] || 1.0 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[pebl]] || 1.01 || || zcluster | | [[pebl]] || 1.01 || || zcluster || || | ||
|- | |- | ||
| [[pfam]] || 26.0 || Database || zcluster || | | [[pfam]] || 26.0 || Database || zcluster || || | ||
|- | |- | ||
| [[Pfam_scan]] || 04282012 || Bioinformatics || zcluster || | | [[Pfam_scan]] || 04282012 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[pftools]] || 2.3.5 || Bioinformatics || zcluster || | | [[pftools]] || 2.3.5 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[phred/phrap/conced]] || || || zcluster || | | [[phred/phrap/conced]] || || || zcluster || || | ||
|- | |- | ||
| [[PhyloBayes]] || 3.3b || Bioinformatics || zcluster || | | [[PhyloBayes]] || 3.3b || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[PHYML]] || 20110919 || Bioinformatics || zcluster || | | [[PHYML]] || 20110919 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[picard]] || 1.62 || Bioinformatics || zcluster || | | [[picard]] || 1.62 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[Populus]] || || Database || zcluster || | | [[Populus]] || || Database || zcluster || || | ||
|- | |- | ||
| [[prank]] || 100802 || Bioinformatics || zcluster || | | [[prank]] || 100802 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[Primer3]] || 2.3.4 || Bioinformatics || zcluster || | | [[Primer3]] || 2.3.4 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[pysam]] || 0.6 || Bioinformatics || zcluster || | | [[pysam]] || 0.6 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[PyTables]] || 2.3.1 || Other || zcluster || | | [[PyTables]] || 2.3.1 || Other || zcluster || || | ||
|- | |- | ||
| [[Qiime]] || 1.6.0 || Bioinformatics || zcluster || | | [[Qiime]] || 1.6.0 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[QTL Cartographer]] || 1.17j || Bioinformatics || zcluster || | | [[QTL Cartographer]] || 1.17j || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[quake]] || 0.3.4 || Bioinformatics || zcluster || | | [[quake]] || 0.3.4 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[Quantum Espresso]] || 5.0.2 || Chemistry || zcluster || | | [[Quantum Espresso]] || 5.0.2 || Chemistry || zcluster || || | ||
|- | |- | ||
| [[R]] || 2.14.0, 2.15.0, 2.15.2 || Statistics || zcluster || Done, SHT | | [[R]] || 2.14.0, 2.15.0, 2.15.2 || Statistics || zcluster || Done, SHT || | ||
|- | |- | ||
| [[R-pcluster]] || 1.9.1, 2.1.1, 2.4.0 || || pcluster || | | [[R-pcluster]] || 1.9.1, 2.1.1, 2.4.0 || || pcluster || || | ||
|- | |- | ||
| [[RAxML]] || 04/26/2012 || Bioinformatics || zcluster || | | [[RAxML]] || 04/26/2012 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[RAxML-Light]] || 1.0.5 || Bioinformatics || zcluster || | | [[RAxML-Light]] || 1.0.5 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[Ray]] || 1.6.1-0 || Bioinformatics || zcluster || | | [[Ray]] || 1.6.1-0 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[RCCBatchBlast]] || 5.0 || Bioinformatics || zcluster || | | [[RCCBatchBlast]] || 5.0 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[RCCBatchBlastPlus]] || 1.0 || Bioinformatics || zcluster || Working, | | [[RCCBatchBlastPlus]] || 1.0 || Bioinformatics || zcluster || Working, YH || | ||
|- | |- | ||
| [[RECON]] || 1.05 || Bioinformatics || zcluster || | | [[RECON]] || 1.05 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[Refseq]] || || Database || zcluster || | | [[Refseq]] || || Database || zcluster || || | ||
|- | |- | ||
| [[Repeatmasker]] || 3.3 || Bioinformatics || zcluster || | | [[Repeatmasker]] || 3.3 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[RepeatScout]] || 1.05 || Bioinformatics || zcluster || | | [[RepeatScout]] || 1.05 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[riboPicker]] || 0.4.3 || Bioinformatics || zcluster || | | [[riboPicker]] || 0.4.3 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[Rice TIGR]] || || Database || zcluster || | | [[Rice TIGR]] || || Database || zcluster || || | ||
|- | |- | ||
| [[RMBlast]] || 2.2.27 || Bioinformatics || zcluster || | | [[RMBlast]] || 2.2.27 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[Rmpi]] || 0.5-9 || Statistics || zcluster || | | [[Rmpi]] || 0.5-9 || Statistics || zcluster || || | ||
|- | |- | ||
| [[RNAz]] || 2.1 || Bioinformatics || zcluster || | | [[RNAz]] || 2.1 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[rnnotator]] || 2.4.12 || Bioinformatics || zcluster || | | [[rnnotator]] || 2.4.12 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[Roche]] || 2.6 || Bioinformatics || zcluster || | | [[Roche]] || 2.6 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[Roseobacter]] || || Database || zcluster || | | [[Roseobacter]] || || Database || zcluster || || | ||
|- | |- | ||
| [[RSAT]] || 1.0 || Bioinformatics || zcluster || | | [[RSAT]] || 1.0 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[RSEM]] || 1.1.21, 1.2.0 || Bioinformatics || zcluster || | | [[RSEM]] || 1.1.21, 1.2.0 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[RTD]] || git at 11/28/2012 || Bioinformatics || zcluster || | | [[RTD]] || git at 11/28/2012 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[RUM]] || 1.11 || Bioinformatics || zcluster || | | [[RUM]] || 1.11 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[Sage]] || 3.1.1, 3.4.1 || Other || zcluster || | | [[Sage]] || 3.1.1, 3.4.1 || Other || zcluster || || | ||
|- | |- | ||
| [[samtools]] || 0.1.18 || Bioinformatics || zcluster || | | [[samtools]] || 0.1.18 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[SAS]] || 9.1 || Statistics || zcluster || | | [[SAS]] || 9.1 || Statistics || zcluster || || | ||
|- | |- | ||
| [[SATé]] || 2.2.4 || Bioinformatics || zcluster || | | [[SATé]] || 2.2.4 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[SEQuel]] || 1.0.2 || Bioinformatics || zcluster || | | [[SEQuel]] || 1.0.2 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[SHE-RA]] || 012012 || Bioinformatics || zcluster || | | [[SHE-RA]] || 012012 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[SHORE]] || 0.8 || Bioinformatics || zcluster || | | [[SHORE]] || 0.8 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[sickle]] || 1.200 || Bioinformatics || zcluster || | | [[sickle]] || 1.200 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[Silva]] || || Database || zcluster || | | [[Silva]] || || Database || zcluster || || | ||
|- | |- | ||
| [[SiZer]] || 07022012 || Bioinformatics || zcluster || | | [[SiZer]] || 07022012 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[slclust]] || 04282012 || Bioinformatics || zcluster || | | [[slclust]] || 04282012 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[SNAP]] || 2010-7-28 || Bioinformatics || zcluster || | | [[SNAP]] || 2010-7-28 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[snow]] || 0.3-8 || Statistics || zcluster || | | [[snow]] || 0.3-8 || Statistics || zcluster || || | ||
|- | |- | ||
| [[snowhite]] || 1.1.4 || Bioinformatics || zcluster || | | [[snowhite]] || 1.1.4 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[snpEff]] || 2_0_5d || Bioinformatics || zcluster || | | [[snpEff]] || 2_0_5d || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[SOAPdenovo]] || 1.05 || Bioinformatics || zcluster || | | [[SOAPdenovo]] || 1.05 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[SOAPdenovo-trans]] || 1.01 || Bioinformatics || zcluster || | | [[SOAPdenovo-trans]] || 1.01 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[SOAPdenovo2]] || r223 || Bioinformatics || zcluster || | | [[SOAPdenovo2]] || r223 || Bioinformatics || zcluster || || | ||
|- | |- | ||
| [[SomaticCall]] || 42811 || Bioinformatics || zcluster || Working, JKP | | [[SomaticCall]] || 42811 || Bioinformatics || zcluster || Working, JKP || | ||
|- | |- | ||
| [[spimap]] || 1.1 || Bioinformatics || zcluster || JKP | | [[spimap]] || 1.1 || Bioinformatics || zcluster || JKP || | ||
|- | |- | ||
| [[SpliceGrapher]] || 0.2.0 || Bioinformatics || zcluster || JKP | | [[SpliceGrapher]] || 0.2.0 || Bioinformatics || zcluster || JKP || | ||
|- | |- | ||
| [[SSAHA2]] || 2.5.5 || Bioinformatics || zcluster || JKP | | [[SSAHA2]] || 2.5.5 || Bioinformatics || zcluster || JKP || | ||
|- | |- | ||
| [[SSPACE]] || 2.0 || Bioinformatics || zcluster || JKP | | [[SSPACE]] || 2.0 || Bioinformatics || zcluster || JKP || | ||
|- | |- | ||
| [[stacks]] || 0.9993, 0.9996 || Bioinformatics || | | [[stacks]] || 0.9993, 0.9996 || Bioinformatics || || || | ||
|- | |- | ||
| [[STEM]] || 2.0 || Bioinformatics || zcluster || JKP | | [[STEM]] || 2.0 || Bioinformatics || zcluster || JKP || | ||
|- | |- | ||
| [[strauto]] || 0.3.1 || Bioinformatics || zcluster || JKP | | [[strauto]] || 0.3.1 || Bioinformatics || zcluster || JKP || | ||
|- | |- | ||
| [[structure]] || 2.3.3 || Bioinformatics || zcluster || JKP | | [[structure]] || 2.3.3 || Bioinformatics || zcluster || JKP || | ||
|- | |- | ||
| [[Sus_scrofa]] || || Database || zcluster || | | [[Sus_scrofa]] || || Database || zcluster || || | ||
|- | |- | ||
| [[SVDetect]] || r0.7m || Bioinformatics || zcluster || JKP ? | | [[SVDetect]] || r0.7m || Bioinformatics || zcluster || JKP ? || | ||
|- | |- | ||
| [[SWIG]] || 2.0.5 || Utilities || zcluster || | | [[SWIG]] || 2.0.5 || Utilities || zcluster || || | ||
|- | |- | ||
| [[T-Coffee]] || 9.03.r1318 || Bioinformatics || zcluster || JKP | | [[T-Coffee]] || 9.03.r1318 || Bioinformatics || zcluster || JKP || | ||
|- | |- | ||
| [[tabix]] || 0.2.5 || Bioinformatics || zcluster || JKP | | [[tabix]] || 0.2.5 || Bioinformatics || zcluster || JKP || | ||
|- | |- | ||
| [[tagdust]] || 1.12 || Bioinformatics || zcluster || JKP ? | | [[tagdust]] || 1.12 || Bioinformatics || zcluster || JKP ? || | ||
|- | |- | ||
| [[tassel]] || 4.0 || Bioinformatics || zcluster || JKP | | [[tassel]] || 4.0 || Bioinformatics || zcluster || JKP || | ||
|- | |- | ||
| [[tgicl]] || 2.1 || Bioinformatics || zcluster || JKP | | [[tgicl]] || 2.1 || Bioinformatics || zcluster || JKP || | ||
|- | |- | ||
| [[TIGER]] || 1.02 || Bioinformatics || zcluster || JKP | | [[TIGER]] || 1.02 || Bioinformatics || zcluster || JKP || | ||
|- | |- | ||
| [[tophat]] || 2.0.5 || Bioinformatics || zcluster || JKP | | [[tophat]] || 2.0.5 || Bioinformatics || zcluster || JKP || | ||
|- | |- | ||
| [[Tracer]] || v 1.5 || Bioinformatics || zcluster || JKP | | [[Tracer]] || v 1.5 || Bioinformatics || zcluster || JKP || | ||
|- | |- | ||
| [[Trinity]] || r2012-10-05 || Bioinformatics || zcluster || JKP | | [[Trinity]] || r2012-10-05 || Bioinformatics || zcluster || JKP || | ||
|- | |- | ||
| [[UNAFold]] || 3.8 || Bioinformatics || zcluster || JKP ? | | [[UNAFold]] || 3.8 || Bioinformatics || zcluster || JKP ? || | ||
|- | |- | ||
| [[Uniprot]] || || Database || zcluster || | | [[Uniprot]] || || Database || zcluster || || | ||
|- | |- | ||
| [[Uniref]] || || Database || zcluster || | | [[Uniref]] || || Database || zcluster || || | ||
|- | |- | ||
| [[usearch]] || v6.0.30 || Bioinformatics || zcluster || JKP | | [[usearch]] || v6.0.30 || Bioinformatics || zcluster || JKP || | ||
|- | |- | ||
| [[vcftools]] || 0.1.10 || Bioinformatics || zcluster || Done, JKP; reviewed by YH | | [[vcftools]] || 0.1.10 || Bioinformatics || zcluster || Done, JKP;|| reviewed by YH | ||
|- | |- | ||
| [[velvet]] || 1.2.01 || Bioinformatics || zcluster || JKP | | [[velvet]] || 1.2.01 || Bioinformatics || zcluster || JKP || | ||
|- | |- | ||
| [[VelvetOptimiser]] || 2.2.4 || Bioinformatics || zcluster || JKP | | [[VelvetOptimiser]] || 2.2.4 || Bioinformatics || zcluster || JKP || | ||
|- | |- | ||
| [[ViennaRNA]] || 1.8.5 || Bioinformatics || zcluster || JKP | | [[ViennaRNA]] || 1.8.5 || Bioinformatics || zcluster || JKP || | ||
|- | |- | ||
| [[vmatch]] || 2.1.6 || Bioinformatics || zcluster || JKP | | [[vmatch]] || 2.1.6 || Bioinformatics || zcluster || JKP || | ||
|- | |- | ||
| [[VMD]] || 1.9.1 || Chemistry || zcluster || | | [[VMD]] || 1.9.1 || Chemistry || zcluster || || | ||
|- | |- | ||
| [[wigToBigWig]] || v 4 || Bioinformatics || zcluster || JKP | | [[wigToBigWig]] || v 4 || Bioinformatics || zcluster || JKP || | ||
|- | |- | ||
| [[WISE2]] || 2.2.0 || Bioinformatics || zcluster || JKP | | [[WISE2]] || 2.2.0 || Bioinformatics || zcluster || JKP || | ||
|- | |- | ||
| [[WU Blast]] || 2.2.6 || Bioinformatics || zcluster || JKP | | [[WU Blast]] || 2.2.6 || Bioinformatics || zcluster || JKP || | ||
|- | |- | ||
| [[yasra]] || 2.3 || Bioinformatics || zcluster || JKP | | [[yasra]] || 2.3 || Bioinformatics || zcluster || JKP || | ||
|- | |- | ||
| [[Zz-example]] || 0.0 || Bioinformatics || zcluster || example for bioinformatics YH | | [[Zz-example]] || 0.0 || Bioinformatics || zcluster || example for bioinformatics YH || | ||
|- | |- | ||
| [[Zz-template]] || 0.0 || Bioinformatics || zcluster || Template for bioinformatics YH | | [[Zz-template]] || 0.0 || Bioinformatics || zcluster || Template for bioinformatics YH || | ||
|- | |- | ||
|} | |} | ||
[[Category:Zcluster]][[Category:Pcluster]] | [[Category:Zcluster]][[Category:Pcluster]] |
Revision as of 16:35, 6 February 2013
Installed Software List
Last updated 2013-02-06.
Note: Click on the icons to the right of the column headings to sort the table.
Name | Version | Category | Cluster | Notes | Reviewed By |
---|---|---|---|---|---|
00-Skipped Page | 0.0 | Work Log | GACRC | YH Created | |
3D_DOCK | 2.0 | Chemistry | pcluster | Ignored by SMW, | YH reviewed, need SHT review |
454 Software | Bioinformatics | zcluster | Done, SMW | ||
aaarf | 1.0.0 | Bioinformatics | zcluster | Done, SMW | |
ABINIT | 6.12.1 | Chemistry | zcluster | Done, SMW | |
ABySS | 1.3.4 | Bioinformatics | zcluster | Done, SMW | |
ALLPATHS-LG | 44254 | Bioinformatics | zcluster | Contains Dead Links, SMW | |
AMBER | 11, 12 | Chemistry | zcluster | Done, SHT | |
AMBER-pcluster | 8 | Chemistry | pcluster | ||
amos | 3.1.0 | Bioinformatics | zcluster | Done, SMW | |
Arabidopsis | Database | zcluster | |||
ARB | 5.3 | Bioinformatics | zcluster | ?, Please Review Running Program Section, SMW | Done, YH reviewed |
Arb | Database | zcluster | |||
AUGUSTUS | 2.5.5 | Bioinformatics | zcluster | Please verify Documentation Section, SMW | |
Bacteria NCBI | Database | zcluster | |||
bam2fastq | 1.1.0 | Bioinformatics | zcluster | Done, SMW | |
BEAST | 1.7.2 | Bioinformatics | zcluster | Done, with Dead Links, SMW | |
BEDTools | 2.16.2 | Bioinformatics | zcluster | ||
BEST Bayesian | 2.3.1 | 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 | ||
Bl2seq | Bioinformatics | zcluster | |||
BLAST Databases | Database | zcluster | |||
Blastall | Bioinformatics | zcluster | |||
BLASTCLUST | Bioinformatics | zcluster | |||
Blastpgp | Bioinformatics | zcluster | |||
Blat | 3.5 | Bioinformatics | zcluster | ||
BMGE | 1.1 | Bioinformatics | zcluster | ||
bowtie | 0.12.8 | Bioinformatics | zcluster | ||
bowtie2 | 2.0.0-beta7 | 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 | ||
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 | ||
COG | 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 | ||
cufflinks | 2.0.2 | Bioinformatics | zcluster | ||
cutadapt | 1.1 | Bioinformatics | zcluster | ||
ddRADseq | Bioinformatics | zcluster | |||
DLCoal | 1.0 | Bioinformatics | zcluster | ||
drmma | 0.5 | Other | zcluster | ||
ea-utils | 1.1.2-537 | Bioinformatics | zcluster | ||
edena | 3Dev120626 | Bioinformatics | zcluster | ||
EMBOSS | 6.2.0 | Bioinformatics | zcluster | ||
emmix | 1.3 | Bioinformatics | zcluster | ||
ESTscan | 3.0.3 | Bioinformatics | zcluster | Done, YH | |
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 | ||
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 | ||
FISH | Database | zcluster | |||
FitModel | 0.5.3 | Bioinformatics | zcluster | ||
FLASH | 1.0.3 | Bioinformatics | zcluster | ||
GAMESS | May2012R1 with XMVB 2.0. | Chemistry | zcluster | ||
GAMESS-pcluster | 2007 R6 | 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 | ||
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 | Others | 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 | ||
gnuplot | 4.0, 4.6.0 | Graphics | zcluster | Done, SHT | |
gpu-blast | 1.1 with ncbi-blast-2.2.25+ | Bioinformatics | zcluster | ||
grace | 5.1.22 | Other | zcluster | ||
Gromacs | 4.5.5 | Chemistry | zcluster | Done, SHT | |
gss | Bioinformatics | zcluster | |||
HDF5 | 1.6.4, 1.8.9 | Other | zcluster | ||
Hmmer | 3.0 | Bioinformatics | zcluster | ||
Homo_sapien | Database | zcluster | |||
htgs | Database | zcluster | |||
htseq | 0.5.3p3 | Bioinformatics | zcluster | ||
igb | 6.7.3 | Bioinformatics | zcluster | ||
IGV | 2.1.23 | Bioinformatics | zcluster | ||
IMa | May 06 | Bioinformatics | zcluster | ||
indel-Seq-Gen | 2.02 | Bioinformatics | zcluster | ||
InStruct | 3.2.09 | Bioinformatics | zcluster | ||
iprscan (InterProScan) | 5.0 CR2 | Bioinformatics | zcluster | ||
iscan | 1.0.0 | Bioinformatics | zcluster | ||
Jellyfish | 1.1.5 | Bioinformatics | zcluster | ||
k-link | 03 27, 2009 | Bioinformatics | zcluster | ||
KEGG | Database | 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 | ||
maize | Database | zcluster | |||
maker | 2.10 | Bioinformatics | zcluster | ||
Maple-pcluster | 10.06 | Other | pcluster | ||
MAQ | 0.7.1 | Bioinformatics | zcluster | ||
Mathematica | 5.2 | Other | pcluster | ||
MatLab | R2012a (7.14.0.739) | Other | zcluster | ||
MCL | 12-135 | Bioinformatics | zcluster | ||
MEAD | 2.2.9 | Chemistry | zcluster | ||
Medicago | Database | 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 | ||
MOTECC qmdcp | 90 | Chemistry | zcluster | ||
MOTECC qmdcp pcluster | 90 | Chemistry | pcluster | ||
MOTHUR | 1.28.0 | Bioinformatics | zcluster | ||
mpi4py | 1.3 | Utilities | 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 | Done, YH | |
NCBI Blast + | 2.2.26 | Bioinformatics | zcluster | ||
ncbi blast parsers | Bioinformatics | zcluster | |||
NCBI_database | Bioinformatics | zcluster | |||
NETCDF | 4.1.3 | Other | zcluster | ||
NETCDF-pcluster | 3.5.1, 3.6.2 | Other | pcluster | ||
netlogo | 5.0 | Other | zcluster | ||
Newbler | 2.6 | 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 | ||
numexp | 1.4.2 | Other | zcluster | ||
NWCHEM | 4.7 | Chemistry | pcluster | ||
opal | 2.0.0 | Bioinformatics | zcluster | ||
Open Babel | 2.3.1 | Chemistry | zcluster | ||
OpenBUGS | 3.2.2 | Statistics | 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 | ||
PASHA | 1.0.6 | Bioinformatics | zcluster | ||
PeakSplitter | 1.0 | Bioinformatics | zcluster | ||
pebl | 1.01 | zcluster | |||
pfam | 26.0 | Database | zcluster | ||
Pfam_scan | 04282012 | Bioinformatics | zcluster | ||
pftools | 2.3.5 | Bioinformatics | zcluster | ||
phred/phrap/conced | zcluster | ||||
PhyloBayes | 3.3b | Bioinformatics | zcluster | ||
PHYML | 20110919 | Bioinformatics | zcluster | ||
picard | 1.62 | Bioinformatics | zcluster | ||
Populus | Database | zcluster | |||
prank | 100802 | Bioinformatics | zcluster | ||
Primer3 | 2.3.4 | Bioinformatics | zcluster | ||
pysam | 0.6 | Bioinformatics | zcluster | ||
PyTables | 2.3.1 | Other | zcluster | ||
Qiime | 1.6.0 | Bioinformatics | zcluster | ||
QTL Cartographer | 1.17j | Bioinformatics | zcluster | ||
quake | 0.3.4 | Bioinformatics | zcluster | ||
Quantum Espresso | 5.0.2 | Chemistry | zcluster | ||
R | 2.14.0, 2.15.0, 2.15.2 | Statistics | zcluster | Done, SHT | |
R-pcluster | 1.9.1, 2.1.1, 2.4.0 | pcluster | |||
RAxML | 04/26/2012 | Bioinformatics | zcluster | ||
RAxML-Light | 1.0.5 | Bioinformatics | zcluster | ||
Ray | 1.6.1-0 | Bioinformatics | zcluster | ||
RCCBatchBlast | 5.0 | Bioinformatics | zcluster | ||
RCCBatchBlastPlus | 1.0 | Bioinformatics | zcluster | Working, YH | |
RECON | 1.05 | Bioinformatics | zcluster | ||
Refseq | Database | zcluster | |||
Repeatmasker | 3.3 | Bioinformatics | zcluster | ||
RepeatScout | 1.05 | Bioinformatics | zcluster | ||
riboPicker | 0.4.3 | Bioinformatics | zcluster | ||
Rice TIGR | Database | zcluster | |||
RMBlast | 2.2.27 | Bioinformatics | zcluster | ||
Rmpi | 0.5-9 | Statistics | zcluster | ||
RNAz | 2.1 | Bioinformatics | zcluster | ||
rnnotator | 2.4.12 | Bioinformatics | zcluster | ||
Roche | 2.6 | Bioinformatics | zcluster | ||
Roseobacter | Database | zcluster | |||
RSAT | 1.0 | Bioinformatics | zcluster | ||
RSEM | 1.1.21, 1.2.0 | Bioinformatics | zcluster | ||
RTD | git at 11/28/2012 | Bioinformatics | zcluster | ||
RUM | 1.11 | Bioinformatics | zcluster | ||
Sage | 3.1.1, 3.4.1 | Other | zcluster | ||
samtools | 0.1.18 | Bioinformatics | zcluster | ||
SAS | 9.1 | Statistics | zcluster | ||
SATé | 2.2.4 | Bioinformatics | zcluster | ||
SEQuel | 1.0.2 | Bioinformatics | zcluster | ||
SHE-RA | 012012 | Bioinformatics | zcluster | ||
SHORE | 0.8 | Bioinformatics | zcluster | ||
sickle | 1.200 | Bioinformatics | zcluster | ||
Silva | Database | zcluster | |||
SiZer | 07022012 | Bioinformatics | zcluster | ||
slclust | 04282012 | Bioinformatics | zcluster | ||
SNAP | 2010-7-28 | Bioinformatics | zcluster | ||
snow | 0.3-8 | 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 | Working, JKP | |
spimap | 1.1 | Bioinformatics | zcluster | JKP | |
SpliceGrapher | 0.2.0 | Bioinformatics | zcluster | JKP | |
SSAHA2 | 2.5.5 | Bioinformatics | zcluster | JKP | |
SSPACE | 2.0 | Bioinformatics | zcluster | JKP | |
stacks | 0.9993, 0.9996 | Bioinformatics | |||
STEM | 2.0 | Bioinformatics | zcluster | JKP | |
strauto | 0.3.1 | Bioinformatics | zcluster | JKP | |
structure | 2.3.3 | Bioinformatics | zcluster | JKP | |
Sus_scrofa | Database | zcluster | |||
SVDetect | r0.7m | Bioinformatics | zcluster | JKP ? | |
SWIG | 2.0.5 | Utilities | zcluster | ||
T-Coffee | 9.03.r1318 | Bioinformatics | zcluster | JKP | |
tabix | 0.2.5 | Bioinformatics | zcluster | JKP | |
tagdust | 1.12 | Bioinformatics | zcluster | JKP ? | |
tassel | 4.0 | Bioinformatics | zcluster | JKP | |
tgicl | 2.1 | Bioinformatics | zcluster | JKP | |
TIGER | 1.02 | Bioinformatics | zcluster | JKP | |
tophat | 2.0.5 | Bioinformatics | zcluster | JKP | |
Tracer | v 1.5 | Bioinformatics | zcluster | JKP | |
Trinity | r2012-10-05 | Bioinformatics | zcluster | JKP | |
UNAFold | 3.8 | Bioinformatics | zcluster | JKP ? | |
Uniprot | Database | zcluster | |||
Uniref | Database | zcluster | |||
usearch | v6.0.30 | Bioinformatics | zcluster | JKP | |
vcftools | 0.1.10 | Bioinformatics | zcluster | Done, JKP; | reviewed by YH |
velvet | 1.2.01 | Bioinformatics | zcluster | JKP | |
VelvetOptimiser | 2.2.4 | Bioinformatics | zcluster | JKP | |
ViennaRNA | 1.8.5 | Bioinformatics | zcluster | JKP | |
vmatch | 2.1.6 | Bioinformatics | zcluster | JKP | |
VMD | 1.9.1 | Chemistry | zcluster | ||
wigToBigWig | v 4 | Bioinformatics | zcluster | JKP | |
WISE2 | 2.2.0 | Bioinformatics | zcluster | JKP | |
WU Blast | 2.2.6 | Bioinformatics | zcluster | JKP | |
yasra | 2.3 | Bioinformatics | zcluster | JKP | |
Zz-example | 0.0 | Bioinformatics | zcluster | example for bioinformatics YH | |
Zz-template | 0.0 | Bioinformatics | zcluster | Template for bioinformatics YH |