[Bioperl-l] Bioperl integration of mlagan/lagan

[Stephen Montgomery]

Hi -
I going to send over a Bioperl wrapper/parser for mlagan and lagan.  One 
small problem  
Lagan can pass back the SimpleAlign object but mlagan needs a multiple 
alignment object.
I get this msg when I put it in SimpleAlign

-------------------- WARNING ---------------------
MSG: Replacing one sequence [MLAGAN-TEST-1_aligned/1-247]

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Here it has overwritten one of the alignments in SimpleAlign to enforce 
the only 2 seq MAX rule in the SimpleAlign object.
Is it backwards compatible if I try to fix the SimpleAlign to handle 
multiple alignment?.  Anyone got another quick fix?

Cheers,
Stephen



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Stephen Montgomery
Genome Sciences Centre
Vancouver, BC Canada
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