int_load_trans_mat module

itrails.int_load_trans_mat.load_trans_mat(n_seq)

This functions returns a string matrix for the CTMC.

Parameters:

n_seq (integer) – Number of sequences of the CTMC

itrails.int_load_trans_mat.trans_mat_num(trans_mat, coal, rho)

This function returns a transition matrix given a string matrix whose values are either ‘0’, or ‘R’ or ‘C’ preceeded by a number, corresponding to a multiplication factor for the recombination and the coalescence rate, respectively. The user can specify these two numerical rates. The function calculates the rates in the diagonals as (-1)*rowSums

Parameters:

• trans_mat (string numpy matrix) – Matrix containing coalescent and recombination rates in strings.

• coal (float) – Coalescent rate.

• rho (float) – Recombination rate