[Snic-users] New and faster bioinformatic software: BLAST+, ClustalW, HMMER, Mafft and Muscle.

[Joel Hedlund]

Dear kappa, matter and neolith users,

new and optimised versions of a number of major bioinformatic software 
packages have recently been installed on NSC resources kappa, matter and 
neolith. If you are using these applications you are highly encouraged 
to try these new versions in your projects, as in some cases our 
optimised binaries provide a multiple increase in performance (e.g: 
hmmer/2.3.2-1: 4x faster than previous, muscle/3.8.31: 2x faster than 
official release).

Installed versions:
blast+ 2.2.24
clustalw 2.1
hmmer 2.3.2-1, 3.0 and 3.0-mpi
mafft 6.851
muscle 3.8.31

Documentation is available here:
/software/apps/[application]/README.INSTALLATIONS
/software/apps/[application]/[version]/README.txt

Expert use tips are documented here:
http://snicdocs.nsc.liu.se/wiki/BLAST+
http://snicdocs.nsc.liu.se/wiki/HMMER

The installations conform to NDGF Biogrid Runtime Environments, so any 
previously existing job scripts should be trivially portable.

Standard modules are provided for the software, so to start using it you 
can use e.g:
module add muscle
module add hmmer/2-default
Please consider using the “default” modules for these applications if at 
all possible (see  README.INSTALLATIONS).

Kind regards,
Joel Hedlund, Applications Expert Bioinformatics @ NSC