Branch errors for simulated E. coli datasets. Simulated E. coli trees are shown for medium mutation rate (0.0001 per base per branch). (A) shows branch length errors as bars, with overestimates of branch length above each branch and underestimates below each branch. Maximum overestimate of branch length was 2.15% (bars above each branch) and maximum underestimate was 4.73% (bars below each branch). (B) shows branch SNP errors as bars, with false-positive errors above each branch and false-negative errors below each branch. The maximum FP SNP value is 6 (bars above each branch) and maximum FN SNP value is 23 (bars below each branch). Note that the bar heights have been normalized by the maximum value for each tree and are not comparable across trees. Outlier results from Mugsy were excluded from the branch length plot, and kSNP results are not shown. All genome alignment methods performed similarly on closed genomes, with Mauve and Mugsy exhibiting the best sensitivity (Table 1).