[Bioperl-l] gap characters in SimpleAlign objects

Nathan Haigh nathanhaigh at ukonline.co.uk
Wed Feb 18 08:39:36 EST 2004

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

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 "."


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