Difference between revisions of "Biocluster Applications"
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!Application | !Application | ||
!Installed Version | !Installed Version | ||
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− | |||
− | |||
|- | |- | ||
|454 | |454 | ||
Line 12: | Line 9: | ||
|AbundantOTU+ | |AbundantOTU+ | ||
|0.91b | |0.91b | ||
− | |||
− | |||
− | |||
|- | |- | ||
|abyss | |abyss | ||
Line 57: | Line 51: | ||
|bcbio-nextgen | |bcbio-nextgen | ||
|0.6.5 | |0.6.5 | ||
− | |||
− | |||
− | |||
|- | |- | ||
|bedtools | |bedtools | ||
Line 71: | Line 62: | ||
|- | |- | ||
|blast+ | |blast+ | ||
− | | | + | |2.2.28+ |
|- | |- | ||
|blast-intel | |blast-intel | ||
Line 77: | Line 68: | ||
|- | |- | ||
|blast | |blast | ||
− | | | + | |2.2.26 |
|- | |- | ||
|blast2go | |blast2go | ||
Line 90: | Line 81: | ||
|boost | |boost | ||
|1.54 | |1.54 | ||
− | |||
− | |||
− | |||
|- | |- | ||
|bowtie | |bowtie | ||
Line 98: | Line 86: | ||
|- | |- | ||
|bowtie2 | |bowtie2 | ||
− | | | + | |2.1.0 |
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− | |||
− | |||
|- | |- | ||
|breseq | |breseq | ||
Line 107: | Line 92: | ||
|- | |- | ||
|bwa | |bwa | ||
− | | | + | |0.7.5a |
|- | |- | ||
|cafe | |cafe | ||
− | | | + | |3.0 |
|- | |- | ||
|casava | |casava | ||
Line 116: | Line 101: | ||
|- | |- | ||
|cd-hit | |cd-hit | ||
− | | | + | |4.6.1 |
|- | |- | ||
|cdbfasta | |cdbfasta | ||
Line 128: | Line 113: | ||
|- | |- | ||
|chimera | |chimera | ||
− | | | + | |1.6.2 |
|- | |- | ||
|cisgenome | |cisgenome | ||
Line 143: | Line 128: | ||
|- | |- | ||
|cufflinks | |cufflinks | ||
− | | | + | |2.1.1 |
− | |||
− | |||
− | |||
|- | |- | ||
|cutadapt | |cutadapt | ||
Line 152: | Line 134: | ||
|- | |- | ||
|cytoscape | |cytoscape | ||
− | | | + | |2.8.3 |
|- | |- | ||
|EagleView | |EagleView | ||
Line 158: | Line 140: | ||
|- | |- | ||
|efiest | |efiest | ||
− | | | + | |devel |
|- | |- | ||
|EMBOSS | |EMBOSS | ||
Line 194: | Line 176: | ||
|- | |- | ||
|gatk | |gatk | ||
− | | | + | |2.6-4 |
− | |||
− | |||
− | |||
|- | |- | ||
|gcc | |gcc | ||
Line 218: | Line 197: | ||
|- | |- | ||
|gmap | |gmap | ||
− | | | + | |2013-03-31 |
|- | |- | ||
|gmes | |gmes | ||
Line 236: | Line 215: | ||
|- | |- | ||
|hmmer | |hmmer | ||
− | | | + | |3.0 |
|- | |- | ||
|htseq | |htseq | ||
Line 260: | Line 239: | ||
|- | |- | ||
|infernal | |infernal | ||
− | | | + | |1.1rc2 |
|- | |- | ||
|inparanoid | |inparanoid | ||
|4.1 | |4.1 | ||
− | |||
− | |||
− | |||
|- | |- | ||
|iprscan | |iprscan | ||
|5.45 | |5.45 | ||
− | |||
− | |||
− | |||
|- | |- | ||
|java | |java | ||
Line 278: | Line 251: | ||
|- | |- | ||
|jellyfish | |jellyfish | ||
− | | | + | |1.1.11 |
|- | |- | ||
|khmer | |khmer | ||
Line 305: | Line 278: | ||
|- | |- | ||
|lua | |lua | ||
− | | | + | |5.2.2 |
|- | |- | ||
|MACS | |MACS | ||
− | | | + | |2.0.10 |
|- | |- | ||
|mafft | |mafft | ||
Line 323: | Line 296: | ||
|- | |- | ||
|MEGAN | |MEGAN | ||
− | | | + | |5.1.0 |
|- | |- | ||
|meme | |meme | ||
Line 335: | Line 308: | ||
|- | |- | ||
|MetaVelvet | |MetaVelvet | ||
− | | | + | |1.2.02-kmer245 |
|- | |- | ||
|mfinder | |mfinder | ||
Line 347: | Line 320: | ||
|- | |- | ||
|ModalClust | |ModalClust | ||
− | | | + | |0.3 |
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
|- | |- | ||
|mothur | |mothur | ||
Line 362: | Line 329: | ||
|- | |- | ||
|mpich2 | |mpich2 | ||
− | | | + | |1.5 |
|- | |- | ||
|msort | |msort | ||
Line 372: | Line 339: | ||
|muscle | |muscle | ||
|3.8.31 | |3.8.31 | ||
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− | |||
− | |||
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− | |||
− | |||
− | |||
− | |||
|- | |- | ||
|novocraft | |novocraft | ||
Line 398: | Line 356: | ||
|- | |- | ||
|openmpi | |openmpi | ||
− | | | + | |1.6.3 |
|- | |- | ||
|orthomcl | |orthomcl | ||
− | | | + | |2.0.7 |
|- | |- | ||
|paml | |paml | ||
Line 435: | Line 393: | ||
|phymmbl | |phymmbl | ||
|4.0 | |4.0 | ||
− | |||
− | |||
− | |||
|- | |- | ||
|picard-tools | |picard-tools | ||
Line 446: | Line 401: | ||
|- | |- | ||
|pplacer | |pplacer | ||
− | | | + | |1.1 |
|- | |- | ||
|prank | |prank | ||
Line 452: | Line 407: | ||
|- | |- | ||
|prodigal | |prodigal | ||
− | |2. | + | |2.2 |
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
|- | |- | ||
|python | |python | ||
Line 464: | Line 413: | ||
|- | |- | ||
|qiime | |qiime | ||
− | | | + | |1.7.0 |
− | |||
− | |||
− | |||
|- | |- | ||
|quake | |quake | ||
Line 476: | Line 422: | ||
|- | |- | ||
|quest | |quest | ||
− | | | + | |devel |
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
|- | |- | ||
|R | |R | ||
Line 491: | Line 431: | ||
|- | |- | ||
|ray | |ray | ||
− | | | + | |2.30 |
|- | |- | ||
|rdp_classifier | |rdp_classifier | ||
Line 515: | Line 455: | ||
|- | |- | ||
|samtools | |samtools | ||
− | |0.1.16 | + | |0.1.16 |
+ | |- | ||
+ | |samtools | ||
+ | |0.1.18 | ||
|- | |- | ||
|samtools | |samtools | ||
Line 530: | Line 473: | ||
|- | |- | ||
|smrtanalysis | |smrtanalysis | ||
− | |1.4.0 | + | |1.4.0 |
+ | |- | ||
+ | |smrtanalysis | ||
+ | |2.0.1 | ||
+ | |- | ||
+ | |SnpEff | ||
+ | |3.2 | ||
|- | |- | ||
|SnpEff | |SnpEff | ||
− | | | + | |3.3e |
|- | |- | ||
|SOAP2 | |SOAP2 | ||
Line 548: | Line 497: | ||
|- | |- | ||
|SOAPec | |SOAPec | ||
− | |2.01 | + | |2.01 |
+ | |- | ||
+ | |SOAPec | ||
+ | |2.02 | ||
|- | |- | ||
|SOAPErrorCorrection | |SOAPErrorCorrection |
Revision as of 00:25, 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 |