[EMBOSS] distmat Uncorrected distance > 100

Sumit Middha 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.


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