Question

Which of the following is wrong statement about the maximum likelihood method’s steps?

(a) It starts with an evolutionary model of sequence change that provides estimates of rates of substitution of one base for another

(b) In the beginning there is an evolutionary model of sequence change that provides estimates of transitions and transversions in a set of nucleic acid sequences

(c) The rates of all possible substitutions are chosen so that the base composition differs

(d) The set of sequences is then aligned

This question was posed to me in an international level competition.

The doubt is from The Maximum Likelihood Approach topic in section Phylogenetic Tree Construction Methods and Programs of Bioinformatics

Answer 1

The correct choice is (c) The rates of all possible substitutions are chosen so that the base composition differs

To elaborate: The rates of all possible substitutions are chosen so that the base composition remains the same. The set of sequences is then aligned, and the substitutions in each column are examined for their fit to a set of trees that describe possible phylogenetic relationships among the sequences.