Maximum likelihood (ML) method. Jarno Tuimala Thanks to James McInerney for the slides with a darker background!. Maximum likelihood. Historically a new method (Felsenstein, 1980’s) ML assumes a model of sequence evolution
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Thanks to James McInerney for the slides with a darker background!
Convention dictates that the order of the nucleotides is a,c,g,t
Note: for amino acids, the matrix is a 20 x 20 matrix and for codon-based models, the matrix is 61 x 61
∏ik (frequency*change probability)
0.25*0.9815 = 0.00002289932