[Bioperl-l] Assessing the features of MSA in fasta format

[Vladimir Babenko]

    Hi, 
thank you Jason for the direction in fasta diversity.
  Still I have other question:
So, I've got MSA fasta formatted output from the map
alignment program. Is there any MSA-processing
modules/methods of the kind, when only bare
fasta-output is provided? For example, I need to
identify the fully overlapping sections of alignment,
sequence percentage in that overlap, etc. I believe
it's a kind of thing I should code by myself, but
that's the first natural question which arises when
you suspect that you're after devising a wheel.
   Thank you again,
          Vladimir
         


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