ClustalW on Sun Grid !!

What is ClustalW?

ClustalW is a general purpose multiple sequence alignment program for DNA or proteins.It produces biologically meaningful multiple sequence alignments of divergent sequences. There are three main steps for achieving alignment: pairwise alignment, guide-tree generation and progressive alignment.

Why Clustal-w ?

ClustalW-mpi is an ideal choice for running on Sun Grid as it has inherent support for MPI. In the MPI version of ClustalW, both the pairwise and progressive alignments stages are parallelized.

How to run ClustalW on Sun Grid?

Detailed steps are available on https://clustal-w.dev.java.net/. To run ClustalW on Sun Grid, you would need an account on http://www.network.com. If you don't have an account on Sun Grid, you can request for an account here.

Sample data and example files

To get a head start in running ClustalW, example data files are available on the developer page of ClustalW.

Links:

ClustalW download: ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/
ClustalW MPI home page: http://packages.debian.org/unstable/science/clustalw-mpi
Running ClustalW on Sun Grid: https://clustal-w.dev.java.net

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Hardik Dave

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