Appendix 1—table 1. Average length of tree compatible segments, both in terms of number of consecutive SNPs and number of consecutive nucleotides, for the full E. coli and simulation data, as well as for alignments from which 5% or 10% of potentially homoplasic sites were removed.

Statistic	Average nb. of SNPs			Average nb. of nucleotides
Perc. homoplasies removed	0%	5%	10%	0%	5%	10%
E. coli	7.59	8.79	10.75	123	145	179
$\rho /\mu =0$	32	2757	11606	387	30435	108413
$\rho /\mu =0.001$	32	430	702	371	5020	8396
$\rho /\mu =0.01$	28	57	85	365	733	1158
$\rho /\mu =0.1$	14	16	18	211	256	312
$\rho /\mu =0.3$	8	9	10	135	157	183
$\rho /\mu =1$	5	5	5	88	100	114
$\rho /\mu =10$	3	3	3	57	62	68