package phylogenetics

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phylogenetics
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Codon rate matrix from Muse and Gaut 94

This modules provides functions to build rates matrices for codon evolution following the model proposed by Muse and Gaut 1. The exact formulation follows the parameterization used by Latrille and Lartillot 2.

References:

see https://academic.oup.com/mbe/article/11/5/715/1008710

see https://academic.oup.com/mbe/article/34/1/204/2656188

module NSCodon = Codon.Universal_genetic_code.NS

module NSCodon_rate_matrix : sig ... end

type param = {

nucleotide_rates : Rate_matrix.Nucleotide.t;
nucleotide_stat_dist : Nucleotide.vector;
omega : float;

}

val rate_matrix : param -> NSCodon_rate_matrix.t

val stationary_distribution : param -> NSCodon.vector