[Bioperl-l] gap characters in SimpleAlign objects

Jason Stajich jason at cgt.duhs.duke.edu
Wed Feb 18 09:14:18 EST 2004


On Wed, 18 Feb 2004, Nathan Haigh wrote:

> I've been using the clustalw module for creating alignment, and I've just
> realised that when you output the alignment the gap character is a "." not a
> "-".
> This is most annoying because I am adding support to this module for
> generating trees via clustalw, and clustalw removes these "." characters. Is
> there a method for changing these gap characters to "-". I have seen the
> gap_char method in the SimpleAlign module, but this seems only to designate
> a particular character as a gap character, and does not actually change the
> character.
> Any ideas on how to do this substitution, and where in BioPerl does this
> assignment get made in the first place, since the default gap char for
> clustalw output is "-" not "."
> Thanks
> Nathan
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Jason Stajich
Duke University
jason at cgt.mc.duke.edu

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