Comparison of simulations with and without sequencing error. Sequencing error was simulated using an Illumina-based model. (a) Mean topological error (nRF) is not affected by sequencing error. (b) Mean values of the DF median, first quartile, and third quartile indicate that sequencing error seems to compensate for the underestimation of branch lengths occurring in simulations without sequencing error. However, some branch lengths are overestimated significantly more in simulations with sequencing error than in those without it. The effect of the reference database is apparent even in the context of sequencing error. In each panel, the error measure is averaged over 30 simulations for each combination of simulation parameters with 200 reads and 100-bp mean read length. Vertical error bars show a standard deviation above and below the mean. Data for the rpoB family are shown.