[Biopython-dev] Normalization of Distance Matrices

[Jordan Willis]

Hi,

I have a question about the pairwise distance calculation in the DistanceCalculator under Phylo.TreeConstruction.

It pertains to the normalization.

Line 456.

 return 1 - (score * 1.0 / max_score)


I understand that the goal here is to have a distance between 0 and 1. But couldn’t this be greater than 1 if say score was negative as is allowed in PAM and BLOSUM lookup matrices. Perhaps the entire distance matrix should be computed, then a minimum and maximum derived, and then normalized between 0 and 1 rather than do it on a pairwise basis. What do you think?

Jordan

PS.

I apologize if you are seeing this in duplicate. I sent it to the regular list instead of the dev list which seems more applicable. 
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