[BioRuby] Clustal ALN writer

[Pjotr Prins]

I propose to write an ALN output writer. ALN files show aligned
sequences with additional lines of information (like a match line). I
want to use it to output PAML positive selection sites. This is
the idea:


SEQ1  alignment 1...
SEQ2  alignment 2...
      ...*.:*....***  (match line)
      ...*....*.....  (pos. sel. line)

Do we want such ALN output (I think it is allowed), and can we allow
for the additional output. I have a proposed interface here:
 
  http://github.com/pjotrp/bioruby/commit/7f320781039b56aee991ab72404655fae210e2cb

I notice ClustalW.to_fasta has been obsoleted. But we don't have
to_aln yet, and we need to allow adding match_lines and other
information.

Pj.