Applications for Biology

TACC maintains a core set of applications to support life science investigations in the areas of Genomics & Bioinformatics, Phylogenetics and Molecular Dynamics. You can find a list of all our currently installed applications for bioscience research here. All applications are available as modules and compiled to run optimally on TACC systems. We understand that our software stack will never comprise the entire universe of bioscience applications and users are encouraged to compile and run open source and/or custom codes from their home directories. We are also in the process of developing detailed documentation describing how to run these applications on TACC systems along with guidelines for the most commonly used parameters.

Genomics and Bioinformatics Applications

Name	Version	Ranger	Lonestar
Abyss	1.3.3		X
BEDTools	2.16.1	X	X
BioPerl	1.6.9		X
Bismark	0.72		X
blat	34	X	X
Bowtie	0.12.7	X	X
BWA	0.6.1	X	X
Cufflinks	1.3.0		X
FASTX-Toolkit	0.0.13		X
GATK	1.5.20	X	X
GSNAP	3/20/2012		X
HMMER	3	X	X
Libgtextutils	0.6		X
MAFFT	6.864		X
Maq	0.7.1		X
mpiBLAST	1.6.0		X
MUSCLE	3.8.31		X
NCBI BLAST+	2.2.26	X	X
Newbler	2.6		X
Oases	0.2.06		X
Picard	1.65	X	X
SAMtools	0.1.18	X	X
SHRiMP	2.2.2		X
SOAPdenovo	1.05		X
SRA toolkit	2.1.9	X	X
SSAKE	3.8		X
Tophat	1.4.0		X
Trinityrnaseq	r2012-03-17		X
Velvet	1.2.02		X

Phylogenetics

Name	Version	Ranger	Lonestar
BEAST	1.6.2		X
ClustalW	2.1		X
MrBayes	3.2.0		X
PHYLIP	3.6.9		X
RAxML	7.2.9		X
RAxML-Light	1.06		X
Parsimonator	1.01		X
Phyutility	2.2		X
QuickTree	1.1		X

Molecular Simulation and Docking

Name	Version	Ranger	Lonestar
Amber	11 bugfix 20	X	X
APBS	1.3		X
AutoDock*	4.2	X
Autodock Vina**	1.1.2		X
Desmond*	3.0.3.1	X
GROMACS	4.5.5	X	X
NAMD	2.9b3	X	X

* Package currently only available on Ranger
** Package currently only available on Lonestar