Biocluster Applications: Difference between revisions

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

Revision as of 01:19, 16 February 2014

Application Version
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
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
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