From Carl R. Woese Institute for Genomic Biology - University of Illinois Urbana-Champaign
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| Application
|
Installed Versions
|
| 454
|
2.6, 2.7, 2.8
|
| AbundantOTU+
|
0.91b
|
| abyss
|
1.2.5, 1.3.3, 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, 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, 1.0.0
|
| bowtie2
|
2.0.0-beta6, 2.0.2, 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, 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, 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, 5.45
|
| java
|
1.6.0_41, 1.7.0_06-i386, 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, 1.31.2, 1.32.0, 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, 2.08.03, 3.00.01, 3.00.02, 3.00.05, 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, 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), 2.7.3-sqlite, 2.7.5-galaxy, 3.2.3
|
| qiime
|
1.3.0, 1.5.0, 1.6.0, 1.7.0
|
| quake
|
0.3.4
|
| quast
|
2.2
|
| quest
|
alpha, devel
|
| R
|
2.15.0, 2.15.1, 2.15.2, 3.0.0(default), 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, 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)
|
| speciate_it
|
184(default)
|
| sratoolkit
|
2.1.16
|
| srna-tools
|
20130118
|
| ssaha2
|
2.5.5
|
| stacks
|
0.9996, 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, 2.0.5, 2.0.6, 2.0.7, 2.0.8, 2.0.10(default)
|
| treemix
|
1.12
|
| trf
|
4.04
|
| trimmomatic
|
0.22, 0.27, 0.30
|
| trinityrnaseq-intel
|
r2013-02-25
|
| trinityrnaseq
|
r2012-06-08, r2013-02-25, r2013-08-14
|
| trinotate
|
trinotate_r20130826
|
| truesight
|
0.06
|
| uchime
|
4.2.40
|
| usearch
|
6.0.307, 6.1.544, 7.0.959
|
| USeq
|
8.5.1
|
| vcftools
|
0.1.7, 0.1.11
|
| velvet-kmer245
|
1.2.10
|
| velvet
|
1.1.04, 1.2.08, 1.2.10
|
| velvetOptimiser
|
2.2.5
|
| wessim
|
1.0
|
| wgs
|
7.0
|
| wise
|
2.2.3-rc7
|