Converting amino acid alignment scores into measures of evolutionary time: a simulation study of various relationships.

Abstract excerpt

Amino acid substitution tables are essential for the proper alignment of protein sequences, and alignment scores based on them can be transformed into distance measures by various means. In the simplest case, the negative log of the score is used. This Poisson relationship assumes that all sites are equally likely to change, however. A more accurate relationship would correct for different rates of change at each...

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