>From a quick look at the code:
Longest identity: you're right i.e.
(Identical residues x 100)/(Length of Alignment - Total Number of Gaps
in Alignment)
Shortest identity = number of identical residues * 100 /
length of longest original sequence
The similarity calculations are the same as the 'identical' ones
except that the number of identical residues is replaced by the
number of pairwise comparisons that have a positive score in
the comparison matrix.
HTH
Alan
> Hi all,
>
> I have checked the docs and googled around but I did not find an
> explanation for how the shortest_similarity or shortest_identity is
> calculated by needle (using the -nobrief option).
>
> For longest_identity it seems to be:
>
> (Identical residues x 100)/(Length of Alignment - Total Number of Gaps
> in Alignment)
>
> Thanks and regards,
>
> Marc
>
>
>
>
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