Difference between revisions of "Biocluster Applications"
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| Line 98: | Line 98: | ||
|- | |- | ||
|bowtie2 | |bowtie2 | ||
| − | |2.0.0-beta6, 2.0.2 | + | |2.0.0-beta6, 2.0.2 |
|- | |- | ||
|bowtie2 | |bowtie2 | ||
| − | |2.0.5 | + | |2.0.5, 2.1.0 |
|- | |- | ||
|breseq | |breseq | ||
| Line 110: | Line 110: | ||
|- | |- | ||
|cafe | |cafe | ||
| − | |2.2 | + | |2.2, 3.0 |
| − | |||
| − | |||
| − | |||
|- | |- | ||
|casava | |casava | ||
| Line 146: | Line 143: | ||
|- | |- | ||
|cufflinks | |cufflinks | ||
| − | |1.1.0, 1.3.0 | + | |1.1.0, 1.3.0 |
|- | |- | ||
|cufflinks | |cufflinks | ||
| − | |2.0.2 | + | |2.0.2, 2.1.1 |
|- | |- | ||
|cutadapt | |cutadapt | ||
| Line 197: | Line 194: | ||
|- | |- | ||
|gatk | |gatk | ||
| − | |1.6-5, 1.6-13 | + | |1.6-5, 1.6-13 |
|- | |- | ||
|gatk | |gatk | ||
| − | |2.5-2 | + | |2.5-2, 2.6-4 |
|- | |- | ||
|gcc | |gcc | ||
| Line 311: | Line 308: | ||
|- | |- | ||
|MACS | |MACS | ||
| − | |1.4.2 | + | |1.4.2, 2.0.10 |
| − | |||
| − | |||
| − | |||
|- | |- | ||
|mafft | |mafft | ||
| Line 356: | Line 350: | ||
|- | |- | ||
|mothur | |mothur | ||
| − | |1.8 | + | |1.8, 1.28.0 |
|- | |- | ||
|mothur | |mothur | ||
| − | | | + | |1.31.2, 1.32.0 |
|- | |- | ||
|mothur | |mothur | ||
| − | |1.32. | + | |1.32.1 |
|- | |- | ||
|mpich | |mpich | ||
| Line 380: | Line 374: | ||
|- | |- | ||
|novocraft | |novocraft | ||
| − | |2.08, 2.08.02 | + | |2.08, 2.08.02 |
|- | |- | ||
|novocraft | |novocraft | ||
| − | |2.08.03 | + | |2.08.03, 3.00.01 |
|- | |- | ||
|novocraft | |novocraft | ||
| − | |3.00.02 | + | |3.00.02, 3.00.05 |
|- | |- | ||
|novocraft | |novocraft | ||
| Line 407: | Line 401: | ||
|- | |- | ||
|orthomcl | |orthomcl | ||
| − | |2.0.2 | + | |2.0.2, 2.0.7 |
| − | |||
| − | |||
| − | |||
|- | |- | ||
|paml | |paml | ||
| Line 464: | Line 455: | ||
|- | |- | ||
|python | |python | ||
| − | |2.6.6 | + | |2.6.6, 2.7.3(default) |
|- | |- | ||
|python | |python | ||
| − | |2.7.3 | + | |2.7.3-sqlite, 2.7.5-galaxy |
|- | |- | ||
|python | |python | ||
| − | |2 | + | |3.2.3 |
| − | |||
| − | |||
| − | |||
|- | |- | ||
|qiime | |qiime | ||
| − | |1. | + | |1.3.0, 1.5.0 |
|- | |- | ||
|qiime | |qiime | ||
| − | |1.7.0 | + | |1.6.0, 1.7.0 |
|- | |- | ||
|quake | |quake | ||
| Line 491: | Line 479: | ||
|- | |- | ||
|R | |R | ||
| − | |2.15.0 | + | |2.15.0, 2.15.1 |
|- | |- | ||
|R | |R | ||
| − | | | + | |2.15.2, 3.0.0(default) |
|- | |- | ||
|R | |R | ||
| − | |3.0. | + | |3.0.2 |
|- | |- | ||
|RAxML | |RAxML | ||
| Line 545: | Line 533: | ||
|- | |- | ||
|SnpEff | |SnpEff | ||
| − | |3.2 | + | |3.2, 3.3e |
| − | |||
| − | |||
| − | |||
|- | |- | ||
|SOAP2 | |SOAP2 | ||
Revision as of 00:23, 16 February 2014
| Application | Installed Version |
|---|---|
| 454 | 2.6, 2.7 |
| 454 | 2.8 |
| AbundantOTU+ | 0.91b |
| abyss | 1.2.5, 1.3.3 |
| abyss | 1.3.4 |
| afni | 2011_12_21_2014 |
| allpathslg | 42911 |
| amos | 3.1.0 |
| AmpliconNoise | 1.2.7 |
| art | 20110922 |
| artemis | 14.0 |
| augustus | 2.6.1 |
| b2g4pipe | 2.5 |
| babraham | bioinformatics |
| bali-phy | 2.1.1 |
| bam2fastq | 1.1.0 |
| bamtools | 0.9.0 |
| bcbio-nextgen | 0.6.5 |
| bedtools | 2.10.0, 2.10.1 |
| bedtools | 2.17.0 |
| biodatabase | 1.0 |
| biopieces | 0.48 |
| blast+ | 2.2.25+, 2.2.28+ |
| blast-intel | 2.2.26 |
| blast | 2.2.25, 2.2.26 |
| blast2go | 2.5 |
| blat | 0.34 |
| boost-intel | 1.54 |
| boost | 1.54 |
| bowtie | 0.12.8, 0.12.9 |
| bowtie | 1.0.0 |
| bowtie2 | 2.0.0-beta6, 2.0.2 |
| bowtie2 | 2.0.5, 2.1.0 |
| breseq | 0.24 |
| bwa | 0.5.9, 0.7.5a |
| cafe | 2.2, 3.0 |
| casava | 1.8.2 |
| cd-hit | 4.6, 4.6.1 |
| cdbfasta | 0.99 |
| cegma | v2.4.010312 |
| chance | 1.0 |
| chimera | 1.5.3, 1.6.2 |
| cisgenome | 2.0 |
| ClonalFrame | 1.2 |
| clustalo | 1.2.0 |
| clustalw | 2.1 |
| cufflinks | 1.1.0, 1.3.0 |
| cufflinks | 2.0.2, 2.1.1 |
| cutadapt | 1.2 |
| cytoscape | 2.8.1, 2.8.3 |
| EagleView | 2.2 |
| efiest | alpha, devel |
| EMBOSS | 6.5.7 |
| erange | 3.2.1 |
| estscan | 3.0.3 |
| fasta | 36.3.5d |
| fasta_splitter | 1 |
| fastqc | 0.10.1 |
| fastsimcoal2 | 1.1.1 |
| fasttree | 2.1.7 |
| fastx_toolkit | 0.0.13 |
| findpeaks | 3.1.9.2 |
| freebayes | 0.9.6 |
| gatk | 1.6-5, 1.6-13 |
| gatk | 2.5-2, 2.6-4 |
| gcc | 4.8.1 |
| geneid | 1.0 |
| genomer | 0.0.10 |
| genometools | 1.5.1 |
| gff | 2.1 |
| glimmer | 3.02 |
| gmap | 2011-09-14, 2013-03-31 |
| gmes | v2.3e |
| gnuplot | 4.6.3 |
| graphviz | 2.32.0 |
| gsl | 1.16 |
| hmmer-mpi | 2.32-MPI-0.92 |
| hmmer | 2.3.2, 3.0 |
| htseq | 0.5.4 |
| icc | 2013.5.192 |
| idba-ud | 1.1.0 |
| IGV | 2.1.24 |
| IGVTools | 2.1.24 |
| IMAGE | 2.33 |
| ImageMagick | 6.7.8-9 |
| infernal | 1.1rc1, 1.1rc2 |
| inparanoid | 4.1 |
| iprscan | 4.8, 5.44 |
| iprscan | 5.45 |
| java | 1.6.0_41, 1.7.0_06-i386 |
| java | 1.7.0_07 |
| jellyfish | 1.1.6, 1.1.11 |
| khmer | 2013-05-06 |
| kmergenie | 1.5854 |
| krona | 2.2 |
| lamarc | 2.1.8 |
| last | 278 |
| lastz | 1.02.00 |
| libstree | 0.4.2 |
| LR-TRIRLS | 20060531 |
| lua | 5.1.4, 5.2.2 |
| MACS | 1.4.2, 2.0.10 |
| mafft | 6.953 |
| matlab-runtime | r2012b |
| matlab | 7.11.0.584 |
| mcl | 12-068 |
| MEGAN | 4.70.4, 5.1.0 |
| meme | 4.9.0 |
| MetaGeneMark | 2010 |
| metAMOS | 1.2 |
| MetaVelvet | 1.2.02, 1.2.02-kmer245 |
| mfinder | 1.2 |
| mira | 3.2.1 |
| MOCAT | 1.1 |
| ModalClust | 0.2, 0.3 |
| mothur | 1.8, 1.28.0 |
| mothur | 1.31.2, 1.32.0 |
| mothur | 1.32.1 |
| mpich | 3.0.4 |
| mpich2 | 1.4.1p1, 1.5 |
| msort | 1.0 |
| MUMmer | 3.23 |
| muscle | 3.8.31 |
| novocraft | 2.08, 2.08.02 |
| novocraft | 2.08.03, 3.00.01 |
| novocraft | 3.00.02, 3.00.05 |
| novocraft | 3.02 |
| oasas-kmer245 | 0.2.8 |
| oasas | 0.2.8 |
| OLB | 1.9.4 |
| openmpi-intel | 1.6.3 |
| openmpi | 1.4.3, 1.6.3 |
| orthomcl | 2.0.2, 2.0.7 |
| paml | 4.4 |
| parallel | 20121122 |
| pathway-tools | 16.5 |
| PBJelly | 12.9.14 |
| peaksplitter | 1.0 |
| perfsuite | 1.0.0 |
| perl | 5.16.1 |
| pfamscan | 1.0 |
| phred | 0.020425.c |
| phylip | 3.69 |
| phymmbl | 4.0 |
| picard-tools | 1.34, 1.73 |
| picard-tools | 1.90 |
| polyphen | 2.2.2 |
| pplacer | 1.0, 1.1 |
| prank | 121002 |
| prodigal | 2.0, 2.2 |
| python | 2.6.6, 2.7.3(default) |
| python | 2.7.3-sqlite, 2.7.5-galaxy |
| python | 3.2.3 |
| qiime | 1.3.0, 1.5.0 |
| qiime | 1.6.0, 1.7.0 |
| quake | 0.3.4 |
| quast | 2.2 |
| quest | alpha, devel |
| R | 2.15.0, 2.15.1 |
| R | 2.15.2, 3.0.0(default) |
| R | 3.0.2 |
| RAxML | 7.3.0 |
| ray | 2.20, 2.30 |
| rdp_classifier | 2.5 |
| rdxplorer | 3.2 |
| repeatmasker | 3.28 |
| rockhopper | 1.2 |
| rsa-tools | 2012-10-09 |
| rstudio | 0.97.312 |
| ruby | 1.9.3 |
| samtools | 0.1.16, 0.1.18 |
| samtools | 0.1.19 |
| sam_comp | 0.7 |
| SICER | 1.1 |
| signalp | 4.1 |
| smrtanalysis | 1.4.0, 2.0.1 |
| SnpEff | 3.2, 3.3e |
| SOAP2 | 2.2 |
| SOAPdenovo-Trans | 1.02 |
| SOAPdenovo | 2.04 |
| SOAPdenovo2 | r240 |
| SOAPec | 2.01, 2.02 |
| SOAPErrorCorrection | 0.04 |
| SOAPGapCloser | 1.12 |
| SOAPprepare | 0.1 |
| speciateit | 184(default) |
| speciateit | template |
| speciatetest | 184 |
| speciate_it | 184(default) |
| sratoolkit | 2.1.16 |
| srna-tools | 20130118 |
| ssaha2 | 2.5.5 |
| stacks | 0.9996 |
| stacks | 0.99994 |
| structure | 2.3.4 |
| subread | 3.1.6 |
| supfam | 1.75 |
| tabix | 0.2.6 |
| tcoffee | 10-r1613 |
| tmhmm | 2.0 |
| tophat | 1.4.1 |
| tophat2 | 2.0.4 |
| tophat2 | 2.0.5 |
| tophat2 | 2.0.6 |
| tophat2 | 2.0.7 |
| tophat2 | 2.0.8 |
| tophat2 | 2.0.10(default) |
| treemix | 1.12 |
| trf | 4.04 |
| trimmomatic | 0.22 |
| trimmomatic | 0.27 |
| trimmomatic | 0.30 |
| trinityrnaseq-intel | r2013-02-25 |
| trinityrnaseq | r2012-06-08 |
| trinityrnaseq | r2013-02-25 |
| trinityrnaseq | r2013-08-14 |
| trinotate | trinotate_r20130826 |
| truesight | 0.06 |
| uchime | 4.2.40 |
| usearch | 6.0.307 |
| usearch | 6.1.544 |
| usearch | 7.0.959 |
| USeq | 8.5.1 |
| vcftools | 0.1.7 |
| vcftools | 0.1.11 |
| velvet-kmer245 | 1.2.10 |
| velvet | 1.1.04 |
| velvet | 1.2.08 |
| velvet | 1.2.10 |
| velvetOptimiser | 2.2.5 |
| wessim | 1.0 |
| wgs | 7.0 |
| wise | 2.2.3-rc7 |
