Module Phylogenetics.Nucleotide_processSource

A representation of classical parametric processes on nucleotides

Example usage of functions

Example 1: Computing a rate matrix

  let example_rate_matrix =
    let model = JC69 in
    let rm = rate_matrix model in
    rm (* The computed rate matrix *)

Example 2: Computing the stationary distribution

  let example_stationary_distribution =
    let model = K80 2.0 in
    let sd = stationary_distribution model in
    sd (* The computed stationary distribution *)

Example 3: Sampling a mutation model using HKY85

  let example_hky85_model =
    let rng = Gsl.Rng.make Gsl.Rng.MT19937 in
    let alpha = 0.5 in
    let model = Random.hky85 rng ~alpha in
    model (* The sampled HKY85 mutation model *)

Example 4: Sampling a mutation model using GTR

  let example_gtr_model =
    let rng = Gsl.Rng.make Gsl.Rng.MT19937 in
    let alpha = 1.0 in
    let model = Random.gtr rng ~alpha in
    model (* The sampled GTR mutation model *)