Deprecated. 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.
module type S = sig ... endEvolution model with linear algebra functions to compute stationary distribution and transition matrix diagonalization.
module type S_with_reduction = sig ... endmodule type Rate_matrix = sig ... endmodule type Diagonalizable_rate_matrix = sig ... endmodule Make
(A : Alphabet.S)
(M : Rate_matrix with type mat := A.matrix) :
sig ... endmodule Make_diag
(A : Alphabet.S)
(M :
Diagonalizable_rate_matrix
with type vec := A.vector
and type mat := A.matrix) :
sig ... endmodule type Nucleotide_S_with_reduction =
S_with_reduction
with type vec := Nucleotide.vector
and type mat := Nucleotide.matrixmodule JC69 : Nucleotide_S_with_reduction with type param = unitJukes-Cantor model with analytical diagonalization of transition matrix.
module JC69_numerical : Nucleotide_S_with_reduction with type param = unitJukes-Cantor model with numerical calculation of probability transition matrix
module K80 : Nucleotide_S_with_reduction with type param = floatK80 model with analytical diagonalization of transition matrix (parametrized by kappa)
module K80_numerical : Nucleotide_S_with_reduction with type param = floatK80 model with numerical calculation of probability transition matrix