Clocks | Test Molecular Clock(ML)
This option performs a Maximum Likelihood test of the molecular clock hypothesis for a given tree topology and sequence alignment. (The Molecular Clock Hypothesis means that all tips of the tree are equidistant from the root of the tree.) two log-likelihood values are calculated and displayed, one with and one without the clock hypothesis. The latter will always be larger (note that the numbers are negative, so larger means smaller in absolute value). The statistical significance of the difference may be tested by comparing twice the difference in log-likelihood values to a chi-squared threshold value with s-2 degrees of freedom, where s is the number of sequences in the alignment.