Difference between revisions of "Biocluster Applications"

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!Application
 
!Application
 
!Installed Version
 
!Installed Version
−
|-
 
−
|454
 
−
|2.6, 2.7
 
 
|-
 
|-
 
|454
 
|454
Line 12: Line 9:
 
|AbundantOTU+
 
|AbundantOTU+
 
|0.91b
 
|0.91b
−
|-
 
−
|abyss
 
−
|1.2.5, 1.3.3
 
 
|-
 
|-
 
|abyss
 
|abyss
Line 57: Line 51:
 
|bcbio-nextgen
 
|bcbio-nextgen
 
|0.6.5
 
|0.6.5
−
|-
 
−
|bedtools
 
−
|2.10.0, 2.10.1
 
 
|-
 
|-
 
|bedtools
 
|bedtools
Line 71: Line 62:
 
|-
 
|-
 
|blast+
 
|blast+
−
|2.2.25+, 2.2.28+
+
|2.2.28+
 
|-
 
|-
 
|blast-intel
 
|blast-intel
Line 77: Line 68:
 
|-
 
|-
 
|blast
 
|blast
−
|2.2.25, 2.2.26
+
|2.2.26
 
|-
 
|-
 
|blast2go
 
|blast2go
Line 90: Line 81:
 
|boost
 
|boost
 
|1.54
 
|1.54
−
|-
 
−
|bowtie
 
−
|0.12.8, 0.12.9
 
 
|-
 
|-
 
|bowtie
 
|bowtie
Line 98: Line 86:
 
|-
 
|-
 
|bowtie2
 
|bowtie2
−
|2.0.0-beta6, 2.0.2
+
|2.1.0
−
|-
 
−
|bowtie2
 
−
|2.0.5, 2.1.0
 
 
|-
 
|-
 
|breseq
 
|breseq
Line 107: Line 92:
 
|-
 
|-
 
|bwa
 
|bwa
−
|0.5.9, 0.7.5a
+
|0.7.5a
 
|-
 
|-
 
|cafe
 
|cafe
−
|2.2, 3.0
+
|3.0
 
|-
 
|-
 
|casava
 
|casava
Line 116: Line 101:
 
|-
 
|-
 
|cd-hit
 
|cd-hit
−
|4.6, 4.6.1
+
|4.6.1
 
|-
 
|-
 
|cdbfasta
 
|cdbfasta
Line 128: Line 113:
 
|-
 
|-
 
|chimera
 
|chimera
−
|1.5.3, 1.6.2
+
|1.6.2
 
|-
 
|-
 
|cisgenome
 
|cisgenome
Line 143: Line 128:
 
|-
 
|-
 
|cufflinks
 
|cufflinks
−
|1.1.0, 1.3.0
+
|2.1.1
−
|-
 
−
|cufflinks
 
−
|2.0.2, 2.1.1
 
 
|-
 
|-
 
|cutadapt
 
|cutadapt
Line 152: Line 134:
 
|-
 
|-
 
|cytoscape
 
|cytoscape
−
|2.8.1, 2.8.3
+
|2.8.3
 
|-
 
|-
 
|EagleView
 
|EagleView
Line 158: Line 140:
 
|-
 
|-
 
|efiest
 
|efiest
−
|alpha, devel
+
|devel
 
|-
 
|-
 
|EMBOSS
 
|EMBOSS
Line 194: Line 176:
 
|-
 
|-
 
|gatk
 
|gatk
−
|1.6-5, 1.6-13
+
|2.6-4
−
|-
 
−
|gatk
 
−
|2.5-2, 2.6-4
 
 
|-
 
|-
 
|gcc
 
|gcc
Line 218: Line 197:
 
|-
 
|-
 
|gmap
 
|gmap
−
|2011-09-14, 2013-03-31
+
|2013-03-31
 
|-
 
|-
 
|gmes
 
|gmes
Line 236: Line 215:
 
|-
 
|-
 
|hmmer
 
|hmmer
−
|2.3.2, 3.0
+
|3.0
 
|-
 
|-
 
|htseq
 
|htseq
Line 260: Line 239:
 
|-
 
|-
 
|infernal
 
|infernal
−
|1.1rc1, 1.1rc2
+
|1.1rc2
 
|-
 
|-
 
|inparanoid
 
|inparanoid
 
|4.1
 
|4.1
−
|-
 
−
|iprscan
 
−
|4.8, 5.44
 
 
|-
 
|-
 
|iprscan
 
|iprscan
 
|5.45
 
|5.45
−
|-
 
−
|java
 
−
|1.6.0_41, 1.7.0_06-i386
 
 
|-
 
|-
 
|java
 
|java
Line 278: Line 251:
 
|-
 
|-
 
|jellyfish
 
|jellyfish
−
|1.1.6, 1.1.11
+
|1.1.11
 
|-
 
|-
 
|khmer
 
|khmer
Line 305: Line 278:
 
|-
 
|-
 
|lua
 
|lua
−
|5.1.4, 5.2.2
+
|5.2.2
 
|-
 
|-
 
|MACS
 
|MACS
−
|1.4.2, 2.0.10
+
|2.0.10
 
|-
 
|-
 
|mafft
 
|mafft
Line 323: Line 296:
 
|-
 
|-
 
|MEGAN
 
|MEGAN
−
|4.70.4, 5.1.0
+
|5.1.0
 
|-
 
|-
 
|meme
 
|meme
Line 335: Line 308:
 
|-
 
|-
 
|MetaVelvet
 
|MetaVelvet
−
|1.2.02, 1.2.02-kmer245
+
|1.2.02-kmer245
 
|-
 
|-
 
|mfinder
 
|mfinder
Line 347: Line 320:
 
|-
 
|-
 
|ModalClust
 
|ModalClust
−
|0.2, 0.3
+
|0.3
−
|-
 
−
|mothur
 
−
|1.8, 1.28.0
 
−
|-
 
−
|mothur
 
−
|1.31.2, 1.32.0
 
 
|-
 
|-
 
|mothur
 
|mothur
Line 362: Line 329:
 
|-
 
|-
 
|mpich2
 
|mpich2
−
|1.4.1p1, 1.5
+
|1.5
 
|-
 
|-
 
|msort
 
|msort
Line 372: Line 339:
 
|muscle
 
|muscle
 
|3.8.31
 
|3.8.31
−
|-
 
−
|novocraft
 
−
|2.08, 2.08.02
 
−
|-
 
−
|novocraft
 
−
|2.08.03, 3.00.01
 
−
|-
 
−
|novocraft
 
−
|3.00.02, 3.00.05
 
 
|-
 
|-
 
|novocraft
 
|novocraft
Line 398: Line 356:
 
|-
 
|-
 
|openmpi
 
|openmpi
−
|1.4.3, 1.6.3
+
|1.6.3
 
|-
 
|-
 
|orthomcl
 
|orthomcl
−
|2.0.2, 2.0.7
+
|2.0.7
 
|-
 
|-
 
|paml
 
|paml
Line 435: Line 393:
 
|phymmbl
 
|phymmbl
 
|4.0
 
|4.0
−
|-
 
−
|picard-tools
 
−
|1.34, 1.73
 
 
|-
 
|-
 
|picard-tools
 
|picard-tools
Line 446: Line 401:
 
|-
 
|-
 
|pplacer
 
|pplacer
−
|1.0, 1.1
+
|1.1
 
|-
 
|-
 
|prank
 
|prank
Line 452: Line 407:
 
|-
 
|-
 
|prodigal
 
|prodigal
−
|2.0, 2.2
+
|2.2
−
|-
 
−
|python
 
−
|2.6.6, 2.7.3(default)
 
−
|-
 
−
|python
 
−
|2.7.3-sqlite, 2.7.5-galaxy
 
 
|-
 
|-
 
|python
 
|python
Line 464: Line 413:
 
|-
 
|-
 
|qiime
 
|qiime
−
|1.3.0, 1.5.0
+
|1.7.0
−
|-
 
−
|qiime
 
−
|1.6.0, 1.7.0
 
 
|-
 
|-
 
|quake
 
|quake
Line 476: Line 422:
 
|-
 
|-
 
|quest
 
|quest
−
|alpha, devel
+
|devel
−
|-
 
−
|R
 
−
|2.15.0, 2.15.1
 
−
|-
 
−
|R
 
−
|2.15.2, 3.0.0(default)
 
 
|-
 
|-
 
|R
 
|R
Line 491: Line 431:
 
|-
 
|-
 
|ray
 
|ray
−
|2.20, 2.30
+
|2.30
 
|-
 
|-
 
|rdp_classifier
 
|rdp_classifier
Line 515: Line 455:
 
|-
 
|-
 
|samtools
 
|samtools
−
|0.1.16, 0.1.18
+
|0.1.16
 +
|-
 +
|samtools
 +
|0.1.18
 
|-
 
|-
 
|samtools
 
|samtools
Line 530: Line 473:
 
|-
 
|-
 
|smrtanalysis
 
|smrtanalysis
−
|1.4.0, 2.0.1
+
|1.4.0
 +
|-
 +
|smrtanalysis
 +
|2.0.1
 +
|-
 +
|SnpEff
 +
|3.2
 
|-
 
|-
 
|SnpEff
 
|SnpEff
−
|3.2, 3.3e
+
|3.3e
 
|-
 
|-
 
|SOAP2
 
|SOAP2
Line 548: Line 497:
 
|-
 
|-
 
|SOAPec
 
|SOAPec
−
|2.01, 2.02
+
|2.01
 +
|-
 +
|SOAPec
 +
|2.02
 
|-
 
|-
 
|SOAPErrorCorrection
 
|SOAPErrorCorrection

Revision as of 01:25, 16 February 2014

Application Installed Version
454 2.8
AbundantOTU+ 0.91b
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 2.17.0
biodatabase 1.0
biopieces 0.48
blast+ 2.2.28+
blast-intel 2.2.26
blast 2.2.26
blast2go 2.5
blat 0.34
boost-intel 1.54
boost 1.54
bowtie 1.0.0
bowtie2 2.1.0
breseq 0.24
bwa 0.7.5a
cafe 3.0
casava 1.8.2
cd-hit 4.6.1
cdbfasta 0.99
cegma v2.4.010312
chance 1.0
chimera 1.6.2
cisgenome 2.0
ClonalFrame 1.2
clustalo 1.2.0
clustalw 2.1
cufflinks 2.1.1
cutadapt 1.2
cytoscape 2.8.3
EagleView 2.2
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 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 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 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 1.1rc2
inparanoid 4.1
iprscan 5.45
java 1.7.0_07
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 5.2.2
MACS 2.0.10
mafft 6.953
matlab-runtime r2012b
matlab 7.11.0.584
mcl 12-068
MEGAN 5.1.0
meme 4.9.0
MetaGeneMark 2010
metAMOS 1.2
MetaVelvet 1.2.02-kmer245
mfinder 1.2
mira 3.2.1
MOCAT 1.1
ModalClust 0.3
mothur 1.32.1
mpich 3.0.4
mpich2 1.5
msort 1.0
MUMmer 3.23
muscle 3.8.31
novocraft 3.02
oasas-kmer245 0.2.8
oasas 0.2.8
OLB 1.9.4
openmpi-intel 1.6.3
openmpi 1.6.3
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 1.90
polyphen 2.2.2
pplacer 1.1
prank 121002
prodigal 2.2
python 3.2.3
qiime 1.7.0
quake 0.3.4
quast 2.2
quest devel
R 3.0.2
RAxML 7.3.0
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
Retrieved from "https://help.igb.illinois.edu/index.php?title=Biocluster_Applications&oldid=7495"