[Bioperl-l] Phylip format for phylogeny

[Jason Stajich]

You'd need to write something that would determine where the cutoffs of
your sub-alignment need to be if you are talking about a contiguous slice
of the alignment you want to preserve.

I have something I wrote a long time ago which basically walked out from
the start and end of the alignment and identify the part I want to
include.  This might be something like setting a cutoff % of sequences in
a column which are gapped and then finding either a single or multiple
regions which were of a minimum length and met the gap restriction cutoff.
This seemed to work for my needs - it reduced some of the noise for later
analyses but it definitely an alg that needs tweaking for a specific
question.

Anyways, you can get a slice of contiguous columns with
$aln->slice($start,$end)

There are also cmds to get non-contiguous columns but I'm not sure if that
is what you want.

-jason

On Fri, 17 Oct 2003, Mike Muratet wrote:

> Greetings
>
> In the "there must be a way to do this" department, I am working on a
> phylogeny project, and I would like to take clustalw output, find the
> common aligned region (i.e., the region without gaps) write it out in
> phylip format and use it in one or more of the available phylogeny
> tools. Converting clustalw to phylip format is trivial, but is there a
> way to find and extract a region from all of the sequences in an
> alignment? (I can't find it in the documentation.)
>
> Thanks
>
> Mike

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu