[Bioperl-l] mega next_aln unmatch

Jason Stajich jason at cgt.duhs.duke.edu
Fri Aug 13 10:28:22 EDT 2004

Good call.  Done.

Is anyone even using the mega format parser/writer?  I have not spent much
time making sure it is up to spec once the intial implementation was

On Fri, 13 Aug 2004, Nathan Haigh wrote:

> I've been playing with some of the alignment file formats and I've noticed
> that when a mega file is read in it returns an alignment object that
> contains the the sequences as represented in the mega file (i.e. with dots
> for matched chars etc).
> I'm not sure how all the other alignment format objects return their
> sequences, but wouldn't it make more sense to return the object with the
> chars converted back to sequence chars? i.e. make a call to $aln->unmatch()
> prior to returning the alignment object at the end of mega.pm? I've just
> seen that nexus.pm also makes the same call, so mega.pm should probably also
> be brought into line with this also.
> Regards
> Nathan
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Jason Stajich
Duke University
jason at cgt.mc.duke.edu

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