[Bioperl-l] AlignIO::clustalw match_line query

[Richard Francis]

Dear List,

I wonder if you can help.

I’m having trouble finding out on which criteria the conserved and
semi-conserved substitution decisions for a match line produced from the
match_line function in AlignIO are based.

I note that match_line produces the same output as an alignment match
line would from ClustalW and indeed is used in the AlignIO::clustalw
module, but are the substitution decisions based on the same Venn
diagram at http://www.ebi.ac.uk/Tools/clustalw2/clustalw_help.html#color
ie are they faithful to the generation of the match line from within
ClustalW itself?

I need to know this as part of a paper I’m writing so I would really
appreciate your help with this.

Kind regards and thanks in advance,

Richard Francis
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