Figure 3.

Substitution rates in phylogenies derived from real sequence data. Ratio of estimated (CpG_est) to true (CpG_true) CpG differences and estimated (nCpG_est) to true (nCpG_true) non-CpG differences plotted against increasing sequence divergence for phylogenies derived from real mouse noncoding (a, b) and coding (c, d) sequences. Separate lines show results for different levels of hypermutability (5-fold, 10-fold and 20-fold hypermutability). Each line is composed of is estimated from 80 simulated replicates of an ~8 Mb sequence.