package phylogenetics

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package phylogenetics
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Module Phylogenetics.Site_evolution_modelSource

Compilation of modules implementing evolution models and providing relevant mathematical procedure (eg, exponential of transition matrix); also includes functors to build models from transition matrices.

Sourcemodule type S = sig ... end

Evolution model with linear algebra functions to compute stationary distribution and transition matrix diagonalization.

Sourcemodule type S_with_reduction = sig ... end
Sourcemodule type Rate_matrix = sig ... end
Sourcemodule type Diagonalizable_rate_matrix = sig ... end
Sourcemodule Make (A : Alphabet.S) (M : Rate_matrix with type mat := A.matrix) : sig ... end
Sourcemodule Make_diag (A : Alphabet.S) (M : Diagonalizable_rate_matrix with type vec := A.vector and type mat := A.matrix) : sig ... end
Sourcemodule JC69 : Nucleotide_S_with_reduction with type param = unit

Jukes-Cantor model with analytical diagonalization of transition matrix.

Jukes-Cantor model with numerical calculation of probability transition matrix

Sourcemodule K80 : Nucleotide_S_with_reduction with type param = float

K80 model with analytical diagonalization of transition matrix (parametrized by kappa)

K80 model with numerical calculation of probability transition matrix

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