Bioinformatics Software

DIAG has a variety of bioinformatics analysis tools pre-installed for the convenience of the user community. At this time, each access method has a different complement of software available for use. As the infrastructure continues to mature, we will deploy these applications such that they are available to all access methods. In addition, we will strive to maintain multiple versions of the most popular tools for those projects and users that need them.

Software

Name Version Shell/SSH Ergatis
454 X
abyss 1.3.4 X
allpathslg-42179 X
AmpliconNoise 1.25 X
augustus 2.5.5 X
BatMis 3 X X
bedtools 2.17.0 X
ber 20051118 X
BioPerl 1.6.1 X
blast 2.2.26 X
blat 35 X
bowtie2 2.0.0-beta7 X
bwa 0.6.2 X
cufflinks 2.0.2 X X
cummeRbund 2.0.0 X
dsrc 1.02 X
ELPH 1.0.1 X
EMBOSS 6.5.7 X X
exonerate 2.2.0 X
expat 2.1.0 X
fastx_toolkit 0.0.13 X
fastx_toolkit 0.0.13 X X
fcp 1.0.3 X
fr-hit v0.7-x86_64 X
FragGeneScan 1.16 X X
GeneMarkHMM 2.3d X
glimmer 3.0.2 X
gmap-gsnap 39648 X
gsl 1.9 X
hmmer 3.0 X X
ima 2-8.26.11 X
infernal 1.0.2 X
JAGS 3.2.0 X
jbrowse 1.2.1 X
jellyfish 1.1.4 X X
khmer X
kSNP v2 X
LipoP 1.0a X
mafft 7.029 X
maker 2.15 X
MEGAN 4.7 X
MetaGeneMark X
metAMOS 1.0b-june X
metaphlan 1.7.2 X
MetaVelvet 1.2.02 X
mothur 1.28.0 X
mpich2 1.4.1p1 X
mummer 3.2.3 X
NCBI-Blast 2.2.25+ X
PASA r2012-06-25 X
praze X
prodigal 2.6.0 X
Qiime 1.6.0 X
R 2.15.2 X X
RepeatMasker 3.3.0 X
rmblast 1.2 X
RNAmmer 1.2 X
samtools 0.1.18 X
samtools 0.1.18 X X
scons 2.2.0 X
signalp 4 X
snap 2010-07-28 X
SOAPdenovo 1.05 X
TMHMM 2.0c X
tophat 1.4.0 X X
trf 4.04 X
trinityrnaseq r2012-02-25 X
tRNAscan-SE 1.3.1 X
usearch 6.0.307 X
velvet 1.2.03 X
workflow 3.1.5 X X
WU-Blast 2.2.6 X