[Bioperl-l] Bio::SimpleAlign - Meaning of overall_percentage_identity?

[Giuseppe G.]

Hi,

I would be grateful if you could shed some light on the exact meaning of 
the method overall_percentage_identity in Bio::SimpleAlign.

If I understand correctly, the method works by considering only 
aminoacids that are identical over all the members of the alignment, and 
then averaging over the total number of aminoacids in the sequence. Is 
this correct?

Thank you
Giuseppe
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