Subject: [EMBOSS] distmat Uncorrected distance > 100
From: "Sumit Middha" <smiddha@indiana.edu>
Date: Thu, October 19, 2006 2:59 pm
To: emboss@lists.open-bio.org
Priority: Normal
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Hi,
I tried using distmat from emboss on some alignments
and am getting
scores in excess of 100 (using all default options).
I am not sure how scores can exceed 100.
D = uncorrected distance = p-distance = 1-S
where S = m/(npos + gaps*gap_penalty)
So D is like a percentage and equals number of
substitutions per 100 bases or amino
acids.
Please correct me or point me to an explanation which
will help clarify my doubt.
Thanks,
Sumit
