Biocluster Applications

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), template
speciatetest	184
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