Jukes-Cantor for Proteins

Question

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Can I use Jukes-Cantor to calculate genetic distance when I have two proteins?

For example, if I have two similar proteins without gaps and length of 50, and with number of difference (substitution) of 12, what is the Jukes-Cantor distance for them?

Answer 1

[Brice Sarver]

Jukes-Cantor is a nucleotide model. Although mechanistic models exist, more work has gone into estimating empirical rate matrices for amino acid data. Ziheng Yang's Computational Molecular Evolution covers this pretty well, including the derivation of some nucleotide models for comparison.