RateEstimation.py - utilities for computing rate estimates for codon models.¶

RateEstimation.evaluateCodonPair(codon1, codon2)¶: evaluate differences between codon pair.

RateEstimation.countSubstitutions(pi, Q)¶: count substitituions given a matrix Q and frequencies pi.

RateEstimation.getQMatrix(pi, Rsi, Rsv, Rni, Rnv)¶

build a q matrix.

Diagonal elements are set to the negative of the row sums. The matrix is normalized such that trace of the matrix is -1.

RateEstimation.getRateMatrix(trained_model, terminals=None)¶

return a rate matrix from an xrate grammar.

terminals: return rate matrix and frequencies for these: terminals. If none are given, a dictionaries of matrices and frequencies are returned.

RateEstimation.setFrequencies(model, mali, prefix='')¶

set frequencies in a model according to those observed in data.

prefix: prefix for rate parameters.

Frequencies are labelled: pa0, pc0, …, pa1, pc1, …, pa2, pc2, …

RateEstimation.getDistanceGTR(pi, matrix)¶: obtain distance from a GTR model. see Felsenstein 1994, pp 209