Fig. 4.

The effect of filtering on the relative frequency of long branch attraction tree estimates induced by MSA. Sequences are simulated from a known “Felsenstein-zone” tree following Hossain et al. (2015) under varying root sequence lengths (x axis) and the likelihood of the three alternative topologies around the critical branch are estimated. The probability of the true tree (y axis) is computed as the fraction of the time the true (simulation) trees is recovered from 200 replicates. Inferred lines show results obtained after the application of existing methods, whereas informed lines show the best possible results obtained applying the perfect knowledge of the true (simulated) MSA.