include sig ... endtype t = Amino_acid.matrixval make : (Amino_acid.t -> Amino_acid.t -> float) -> tmake f is a matrix such that f i j is the rate of transition from state i to state j. f is called only for i <> j.
val make_symetric : (Amino_acid.t -> Amino_acid.t -> float) -> tval jc69 : unit -> tval gtr :
stationary_distribution:Amino_acid.vector ->
exchangeabilities:Amino_acid.matrix ->
tGeneralised Time-Reversible model. exchangeabilities should be a symetric matrix with arbitrary diagonal
val stationary_distribution : t -> Amino_acid.vectorstationary_distribution r numerically computes the asymptotic probability distribution pi of the CTMC defined by r.
val scaled_rate_matrix : Amino_acid.vector -> t -> tscaled_rate_matrix pi r is a new matrix rate such that the corresponding CTMC has one expected transition per unit of time. In addition, if r is symetrical, the result has pi as stationary distribution.