Mutation-selection model for codons
This module defines a parameterization for the Mutsel evolutionary model for codons, as well as functions to compute the corresponding transition rate matrix and the associated stationary distribution.
References:
module NSCodon = Codon.Universal_genetic_code.NSmodule NSCodon_rate_matrix : sig ... endtype param = {nucleotide_rates : Rate_matrix.Nucleotide.t;nucleotide_stat_dist : Nucleotide.vector;omega : float;scaled_fitness : Amino_acid.vector;gBGC : float;pps : float;}val random_param :
Gsl.Rng.t ->
nucleotide_process:Nucleotide_process.t ->
alpha:float ->
paramval flat_param : unit -> paramval rate_matrix : param -> NSCodon_rate_matrix.trate_matrix param computes the rate matrix for codon substitutions based on the given parameter values param. The resulting matrix is a rate matrix, meaning that its off-diagonal elements are positive and its lines sum to 0.
Example:
let param = flat_param () in
let matrix = rate_matrix param inval stationary_distribution : param -> NSCodon.vectorstationary_distribution param calculates the stationary distribution under parameter value param.
Example:
let param = flat_param () in
let distribution = stationary_distribution param inval transition_probability_matrix : param -> float -> NSCodon.matrixtransition_probability_matrix param t computes the transition probability matrix for codon substitutions over a specified time period t based on the given parameter values param. The resulting matrix is a probability matrix, meaning that all elements are probabilities and lines sum to 1.
Example:
let param = flat_param () in
let time = 0.1 in
let transition_matrix = transition_probability_matrix param time in