[EMBOSS] distmat Uncorrected distance > 100
Sumit Middha
smiddha at indiana.edu
Thu Oct 19 14:59:57 UTC 2006
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
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