Dear Marc,
I indeed do not see the explanation in the manual, but I did some testing and I
understand that :
- Identity and Similarity are computed by dividing by the total length of the
alignment
- Longest_Identity and Longest_Similarity are computed by dividing by the number
of aligned positions (= total length of the alignment - number of indels)
- Shortest_Identity and Shortest_Similarity are computed by dividing by the
length of the longest sequence
Regards,
Guy Bottu,
Belgian EMBnet Node
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