Fig. 3.

Accuracy of clonal frame estimation from recombining bacterial genomes. The x-axis shows the recombination rate R under which simulations are performed. The y-axis shows the accuracy of inference, as the proportion of branches correctly estimated using the Robinson–Foulds metric (Robinson & Foulds, 1981). Ten independent replicates are used for R = 0.1 and 100 in all other cases. Genomes are 1 Mbp long and the scaled mutation rate is fixed at 0.01. (a) Accuracy of three phylogenetic methods: neighbour-joining (NJ), unweighted pair group method with arithmetic mean (UPGMA) and maximum-likelihood (ML). Error bars represent ± 1 sd. (b) Clonal frame branches were separated into three age categories: young, middle-aged and old (respectively with a distance between the branch mid-point and the root of more than 2.09, between 1.32 and 2.09, and less than 1.32 N_e generations). The ML accuracy for each age category is plotted separately in different colours.