[EMBOSS] Batch alignments?

[Robin Colgrove]

Hello EMBOSS-folk.

Given a set of fasta files, each an ordered list of coding sequences for a set of highly homologous (viral) genomes, is there some straightforward way of generating a file with alignments of the coding sequences other than doing each one manually (around a 100 genes).

That is, if each file is of the form:

>gene1
ATG...
...TAG
>gene2
ATG...
...TAA

etc....

I want to align each set of homologous genes.   I've used matcher and needle to do a gene at a time, but it would be nice to batch this.

thanks,

Robin Colgrove
Harvard Medical School

PS: Embarrassingly enough, I am using v3.0.0 of emboss (Mac OS X 10.6.5). Can I just install a new version or do I have to uninstall everything first? Looking for the minimum fuss route.