[EMBOSS] distmat Uncorrected distance > 100
smiddha at indiana.edu
Thu Oct 19 14:59:57 UTC 2006
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.
More information about the EMBOSS