SCUEAL performance on simulated data.

Scenario provides a brief description a given simulation scenario. Seq., sites lists the number and length of simulated sequences. Type/distance classifies the simulation scenario by type and mean divergence between parental strains, measured as the total branch length (expected number of substitutions/site 100%) between the strains. Inferred Mosaics tabulates the number of cases (and the number of those that matched or bested the BIC score of the correct model) that fell into each of the classification categories (see main text for further detail). Correct: the simulated mosaic was recovered; superset: the simulated mosaic and superfluous breakpoints were inferred; subset: a partial correct mosaic was recapitulated (some breakpoints missing); and M/M - the inferred mosaic was a mismatch with the generating one. Breakpoints enumerates the location of each simulated breakpoint and its parental lineages, the number of times the breakpoint was recovered by SCUEAL, and the median (2.5%–97.5% range) of the distribution of distances between the simulated and inferred breakpoints.