Biocluster Applications: Difference between revisions

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!Version
!Version
|-
|-
|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
|
|-
|-
|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
|-
|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
|}
|}

Revision as of 00:17, 16 February 2014

Application Version
Retrieved from "https://help.igb.illinois.edu/index.php?title=Biocluster_Applications&oldid=7490"