[Bioperl-l] alignment and assembly

[Chad Matsalla]

Jason wrote:
> See the Bio::AlignIO for how to read in alignments from files.  We don't
> interface with phrap or the tigr assembler at this point.

Yes we do.

See Bio::Tools::Alignment::Consed.pm to work with phrap alignments. It
really doesn't do pair-by-pair comparisons but it will help when using
phrap to cluster sequences and things.

If anybody would like to help I would like to create more
bioperl-compliant alignment objects out of consed.pm but at the time I
created it this wasn't an issue.

Chad Matsalla