_build_exp_freq_mat ( exp_freq_table )

Build an expected frequency matrix exp_freq_table: should be a FreqTable instance

_build_log_odds_mat (
        subs_mat,
        logbase=2,
        factor=10.0,
        round_digit=0,
        keep_nd=0,
        )

_build_log_odds_mat(subs_mat,logbase=10,factor=10.0,round_digit=1): Build a log-odds matrix logbase=2: base of logarithm used to build (default 2) factor=10.: a factor by which each matrix entry is multiplied round_digit: roundoff place after decimal point keep_nd: if true, keeps the -999 value for non-determined values (for which there are no substitutions in the frequency substitutions matrix). If false, plants the minimum log-odds value of the matrix in entries containing -999

Build a log-odds matrix

_build_obs_freq_mat ( acc_rep_mat )

build_obs_freq_mat(acc_rep_mat): Build the observed frequency matrix, from an accepted replacements matrix The accRep matrix should be generated by the user.

_build_subs_mat ( obs_freq_mat,  exp_freq_mat )

Build the substitution matrix

Build the substitution matrix

make_log_odds_matrix (
        acc_rep_mat,
        exp_freq_table=None,
        logbase=2,
        factor=1.,
        round_digit=9,
        keep_nd=0,
        )

External function. User provides an accepted replacement matrix, and, optionally the following: expected frequency table, log base, mult. factor, and rounding factor. Generates a log-odds matrix, calling internal SubsMat functions.

two_mat_DJS (
        mat_1,
        mat_2,
        pi_1=0.5,
        pi_2=0.5,
        )

Jensen-Shannon Distance Need to input observed frequency matrices