Software-old: Difference between revisions
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| [[MIRA]] || 3.9.9 || Bioinformatics || zcluster | | [[MIRA]] || 3.9.9 || Bioinformatics || zcluster | ||
|- | |- | ||
| [[pebl]] || 1.01 || | | [[pebl]] || 1.01 || || zcluster | ||
|- | |- | ||
| [[Burrows-Wheeler Aligner (BWA)]] || 0.6.2 || Bioinformatics || zcluster | | [[Burrows-Wheeler Aligner (BWA)]] || 0.6.2 || Bioinformatics || zcluster | ||
Revision as of 00:24, 31 January 2013
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 | Cluster |
|---|---|---|---|
| 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 | Database | zcluster | |
| Blastpgp | Bioinformatics | ||
| Arabidopsis | Database | cluster | |
| Arb | Database | zcluster | |
| Bacteria NCBI | Database | zcluster | |
| COG | zcluster | ||
| NCBI_database | Bioinformatics | zcluster | |
| gss | Bioinformatics | zcluster | |
| FISH | Database | zcluster | |
| Homo_sapien | Database | zcluster | |
| htgs | Database | zcluster | |
| KEGG | Database | zcluster | |
| Medicago | Database | zcluster | |
| Populus | Database | zcluster | |
| Refseq | Database | zcluster | |
| Rice TIGR | Database | zcluster | |
| Roseobacter | Database | zcluster | |
| Silva | Database | zcluster | |
| Sus_scrofa | Database | zcluster | |
| Uniprot | Database | zcluster | |
| Uniref | Database | 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 | zcluster | |
| Burrows-Wheeler Aligner (BWA) | 0.6.2 | Bioinformatics | 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 | zcluster |
| BS Seeker | download at Dec 113 | Bioinformatics | zcluster |
| 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 |