package phylogenetics

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 *)