Difference between revisions of "Biocluster Applications"

From Carl R. Woese Institute for Genomic Biology - University of Illinois Urbana-Champaign
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{| style='width: 900px;  margin: 0 auto' class='wikitable' border='1' cellpadding='1' cellspacing='1'|-||home|-|454|2.6|-|454|2.7|-|454|2.8|-|AbundantOTU+|0.91b|-|abyss|1.2.5|-|abyss|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|-|bedtools|2.10.1|-|bedtools|2.17.0|-|biodatabase|1.0|-|biopieces|0.48|-|blast+|2.2.25+|-|blast+|2.2.28+|-|blast-intel|2.2.26|-|blast|2.2.25|-|blast|2.2.26|-|blast2go|2.5|-|blat|0.34|-|boost-intel|1.54|-|boost|1.54|-|bowtie|0.12.8|-|bowtie|0.12.9|-|bowtie|1.0.0|-|bowtie2|2.0.0-beta6|-|bowtie2|2.0.2|-|bowtie2|2.0.5|-|bowtie2|2.1.0|-|breseq|0.24|-|bwa|0.5.9|-|bwa|0.7.5a|-|cafe|2.2|-|cafe|3.0|-|casava|1.8.2|-|cd-hit|4.6|-|cd-hit|4.6.1|-|cdbfasta|0.99|-|cegma|v2.4.010312|-|chance|1.0|-|chimera|1.5.3|-|chimera|1.6.2|-|cisgenome|2.0|-|ClonalFrame|1.2|-|clustalo|1.2.0|-|clustalw|2.1|-|cufflinks|1.1.0|-|cufflinks|1.3.0|-|cufflinks|2.0.2|-|cufflinks|2.1.1|-|cutadapt|1.2|-|cytoscape|2.8.1|-|cytoscape|2.8.3|-|EagleView|2.2|-|efiest|alpha|-|efiest|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|-|gatk|1.6-13|-|gatk|2.5-2|-|gatk|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|-|gmap|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|-|hmmer|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|-|infernal|1.1rc2|-|inparanoid|4.1|-|iprscan|4.8|-|iprscan|5.44|-|iprscan|5.45|-|java|1.6.0_41|-|java|1.7.0_06-i386|-|java|1.7.0_07|-|jellyfish|1.1.6|-|jellyfish|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|-|lua|5.2.2|-|MACS|1.4.2|-|MACS|2.0.10|-|mafft|6.953|-|matlab-runtime|r2012b|-|matlab|7.11.0.584|-|mcl|12-068|-|MEGAN|4.70.4|-|MEGAN|5.1.0|-|meme|4.9.0|-|MetaGeneMark|2010|-|metAMOS|1.2|-|MetaVelvet|1.2.02|-|MetaVelvet|1.2.02-kmer245|-|mfinder|1.2|-|mira|3.2.1|-|MOCAT|1.1|-|ModalClust|0.2|-|ModalClust|0.3|-|module-cvs||-|module-info||-|modules||-|mothur|1.8|-|mothur|1.28.0|-|mothur|1.31.2|-|mothur|1.32.0|-|mothur|1.32.1|-|mpich|3.0.4|-|mpich2|1.4.1p1|-|mpich2|1.5|-|msort|1.0|-|MUMmer|3.23|-|muscle|3.8.31|-|novocraft|2.08|-|novocraft|2.08.02|-|novocraft|2.08.03|-|novocraft|3.00.01|-|novocraft|3.00.02|-|novocraft|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|-|openmpi|1.6.3|-|orthomcl|2.0.2|-|orthomcl|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|-|picard-tools|1.73|-|picard-tools|1.90|-|polyphen|2.2.2|-|pplacer|1.0|-|pplacer|1.1|-|prank|121002|-|prodigal|2.0|-|prodigal|2.2|-|python|2.6.6|-|python|2.7.3(default)|-|python|2.7.3-sqlite|-|python|2.7.5-galaxy|-|python|3.2.3|-|qiime|1.3.0|-|qiime|1.5.0|-|qiime|1.6.0|-|qiime|1.7.0|-|quake|0.3.4|-|quast|2.2|-|quest|alpha|-|quest|devel|-|R|2.15.0|-|R|2.15.1|-|R|2.15.2|-|R|3.0.0(default)|-|R|3.0.2|-|RAxML|7.3.0|-|ray|2.20|-|ray|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|-|samtools|0.1.18|-|samtools|0.1.19|-|sam_comp|0.7|-|SICER|1.1|-|signalp|4.1|-|smrtanalysis|1.4.0|-|smrtanalysis|2.0.1|-|SnpEff|3.2|-|SnpEff|3.3e|-|SOAP2|2.2|-|SOAPdenovo-Trans|1.02|-|SOAPdenovo|2.04|-|SOAPdenovo2|r240|-|SOAPec|2.01|-|SOAPec|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|-|template||-|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|-|version||-|wessim|1.0|-|wgs|7.0|-|wise|2.2.3-rc7|}
+
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|-
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|454
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|-
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|-
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|-
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|-
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|-
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|-
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|-
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|-
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|-
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|-
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|-
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|-
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|-
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|-
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|-
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|estscan
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|-
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|-
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|-
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|-
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|-
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|-
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|-
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|-
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|-
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|-
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|-
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|-
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|-
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|0.0.10
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|-
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|-
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|-
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|3.02
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|-
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|-
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|-
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|-
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|-
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|-
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|-
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|-
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|-
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|-
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|-
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|-
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|-
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|-
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|-
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|-
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|1.1rc2
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|-
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|-
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|-
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|5.44
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|-
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|iprscan
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|5.45
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|-
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|-
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|-
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|-
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|-
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|1.1.11
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|-
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|2013-05-06
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|-
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|1.5854
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|-
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|2.2
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|-
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|2.1.8
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|-
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|-
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|-
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|-
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|-
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|-
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|-
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|-
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|12-068
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|-
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|-
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|MEGAN
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|5.1.0
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|-
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|meme
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|4.9.0
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|-
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|MetaGeneMark
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|2010
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|-
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|-
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|1.2.02
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|-
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|MetaVelvet
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|-
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|-
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|
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|-
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|
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|
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|-
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|1.8
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|-
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|1.28.0
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|-
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|1.31.2
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|-
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|1.32.0
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|-
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|3.0.4
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|-
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|1.4.1p1
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|-
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|mpich2
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|1.5
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|-
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|1.0
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|-
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|3.23
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|-
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|3.8.31
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|-
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|novocraft
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|2.08
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|-
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|novocraft
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|2.08.02
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|-
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|novocraft
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|2.08.03
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|-
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|novocraft
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|3.00.01
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|-
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|novocraft
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|3.00.02
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|-
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|novocraft
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|3.00.05
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|-
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|3.02
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|-
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|oasas-kmer245
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|0.2.8
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|-
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|oasas
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|0.2.8
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|-
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|OLB
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|1.9.4
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|-
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|1.6.3
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|-
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|-
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|1.6.3
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|-
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|orthomcl
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|2.0.2
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|-
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|orthomcl
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|2.0.7
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|-
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|paml
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|4.4
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|-
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|parallel
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|20121122
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|-
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|pathway-tools
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|16.5
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|-
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|PBJelly
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|12.9.14
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|-
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|peaksplitter
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|1.0
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|-
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|perfsuite
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|1.0.0
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|-
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|perl
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|5.16.1
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|-
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|pfamscan
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|1.0
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|-
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|phred
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|0.020425.c
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|-
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|phylip
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|3.69
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|-
 +
|phymmbl
 +
|4.0
 +
|-
 +
|picard-tools
 +
|1.34
 +
|-
 +
|picard-tools
 +
|1.73
 +
|-
 +
|picard-tools
 +
|1.90
 +
|-
 +
|polyphen
 +
|2.2.2
 +
|-
 +
|pplacer
 +
|1.0
 +
|-
 +
|pplacer
 +
|1.1
 +
|-
 +
|prank
 +
|121002
 +
|-
 +
|prodigal
 +
|2.0
 +
|-
 +
|prodigal
 +
|2.2
 +
|-
 +
|python
 +
|2.6.6
 +
|-
 +
|python
 +
|2.7.3(default)
 +
|-
 +
|python
 +
|2.7.3-sqlite
 +
|-
 +
|python
 +
|2.7.5-galaxy
 +
|-
 +
|python
 +
|3.2.3
 +
|-
 +
|qiime
 +
|1.3.0
 +
|-
 +
|qiime
 +
|1.5.0
 +
|-
 +
|qiime
 +
|1.6.0
 +
|-
 +
|qiime
 +
|1.7.0
 +
|-
 +
|quake
 +
|0.3.4
 +
|-
 +
|quast
 +
|2.2
 +
|-
 +
|quest
 +
|alpha
 +
|-
 +
|quest
 +
|devel
 +
|-
 +
|R
 +
|2.15.0
 +
|-
 +
|R
 +
|2.15.1
 +
|-
 +
|R
 +
|2.15.2
 +
|-
 +
|R
 +
|3.0.0(default)
 +
|-
 +
|R
 +
|3.0.2
 +
|-
 +
|RAxML
 +
|7.3.0
 +
|-
 +
|ray
 +
|2.20
 +
|-
 +
|ray
 +
|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
 +
|-
 +
|samtools
 +
|0.1.18
 +
|-
 +
|samtools
 +
|0.1.19
 +
|-
 +
|sam_comp
 +
|0.7
 +
|-
 +
|SICER
 +
|1.1
 +
|-
 +
|signalp
 +
|4.1
 +
|-
 +
|smrtanalysis
 +
|1.4.0
 +
|-
 +
|smrtanalysis
 +
|2.0.1
 +
|-
 +
|SnpEff
 +
|3.2
 +
|-
 +
|SnpEff
 +
|3.3e
 +
|-
 +
|SOAP2
 +
|2.2
 +
|-
 +
|SOAPdenovo-Trans
 +
|1.02
 +
|-
 +
|SOAPdenovo
 +
|2.04
 +
|-
 +
|SOAPdenovo2
 +
|r240
 +
|-
 +
|SOAPec
 +
|2.01
 +
|-
 +
|SOAPec
 +
|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
 +
|-
 +
|template
 +
|
 +
|-
 +
|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
 +
|-
 +
|version
 +
|
 +
|-
 +
|wessim
 +
|1.0
 +
|-
 +
|wgs
 +
|7.0
 +
|-
 +
|wise
 +
|2.2.3-rc7
 +
|}

Revision as of 22:14, 15 February 2014

home
454 2.6
454 2.7
454 2.8
AbundantOTU+ 0.91b
abyss 1.2.5
abyss 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
bedtools 2.10.1
bedtools 2.17.0
biodatabase 1.0
biopieces 0.48
blast+ 2.2.25+
blast+ 2.2.28+
blast-intel 2.2.26
blast 2.2.25
blast 2.2.26
blast2go 2.5
blat 0.34
boost-intel 1.54
boost 1.54
bowtie 0.12.8
bowtie 0.12.9
bowtie 1.0.0
bowtie2 2.0.0-beta6
bowtie2 2.0.2
bowtie2 2.0.5
bowtie2 2.1.0
breseq 0.24
bwa 0.5.9
bwa 0.7.5a
cafe 2.2
cafe 3.0
casava 1.8.2
cd-hit 4.6
cd-hit 4.6.1
cdbfasta 0.99
cegma v2.4.010312
chance 1.0
chimera 1.5.3
chimera 1.6.2
cisgenome 2.0
ClonalFrame 1.2
clustalo 1.2.0
clustalw 2.1
cufflinks 1.1.0
cufflinks 1.3.0
cufflinks 2.0.2
cufflinks 2.1.1
cutadapt 1.2
cytoscape 2.8.1
cytoscape 2.8.3
EagleView 2.2
efiest alpha
efiest 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
gatk 1.6-13
gatk 2.5-2
gatk 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
gmap 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
hmmer 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
infernal 1.1rc2
inparanoid 4.1
iprscan 4.8
iprscan 5.44
iprscan 5.45
java 1.6.0_41
java 1.7.0_06-i386
java 1.7.0_07
jellyfish 1.1.6
jellyfish 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
lua 5.2.2
MACS 1.4.2
MACS 2.0.10
mafft 6.953
matlab-runtime r2012b
matlab 7.11.0.584
mcl 12-068
MEGAN 4.70.4
MEGAN 5.1.0
meme 4.9.0
MetaGeneMark 2010
metAMOS 1.2
MetaVelvet 1.2.02
MetaVelvet 1.2.02-kmer245
mfinder 1.2
mira 3.2.1
MOCAT 1.1
ModalClust 0.2
ModalClust 0.3
module-cvs
module-info
modules
mothur 1.8
mothur 1.28.0
mothur 1.31.2
mothur 1.32.0
mothur 1.32.1
mpich 3.0.4
mpich2 1.4.1p1
mpich2 1.5
msort 1.0
MUMmer 3.23
muscle 3.8.31
novocraft 2.08
novocraft 2.08.02
novocraft 2.08.03
novocraft 3.00.01
novocraft 3.00.02
novocraft 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
openmpi 1.6.3
orthomcl 2.0.2
orthomcl 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
picard-tools 1.73
picard-tools 1.90
polyphen 2.2.2
pplacer 1.0
pplacer 1.1
prank 121002
prodigal 2.0
prodigal 2.2
python 2.6.6
python 2.7.3(default)
python 2.7.3-sqlite
python 2.7.5-galaxy
python 3.2.3
qiime 1.3.0
qiime 1.5.0
qiime 1.6.0
qiime 1.7.0
quake 0.3.4
quast 2.2
quest alpha
quest devel
R 2.15.0
R 2.15.1
R 2.15.2
R 3.0.0(default)
R 3.0.2
RAxML 7.3.0
ray 2.20
ray 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
samtools 0.1.18
samtools 0.1.19
sam_comp 0.7
SICER 1.1
signalp 4.1
smrtanalysis 1.4.0
smrtanalysis 2.0.1
SnpEff 3.2
SnpEff 3.3e
SOAP2 2.2
SOAPdenovo-Trans 1.02
SOAPdenovo 2.04
SOAPdenovo2 r240
SOAPec 2.01
SOAPec 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
template
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
version
wessim 1.0
wgs 7.0
wise 2.2.3-rc7
Retrieved from "https://help.igb.illinois.edu/index.php?title=Biocluster_Applications&oldid=7433"