Fig. 3

This figure shows a mutation matrix with one false negative (in blue), one false positive (in red), and one missing entry. The first step indicates how each mutation (column in the matrix) corresponds to an unrooted tree with at most one internal branch. The second step is to estimate the phylogeny by applying a quartet-based method. This approach is motivated by there being no anomalous quartets under the \(\texttt {IS+UEM}\) model, assuming \(\alpha + \beta \ne 1\) (Theorem 1)