Detecting mosaic structures in DNA sequence alignments

This article first provides a concise introduction to the statistical approach to phyloge- netics. It then describes a new method for detecting mosaic structures in DNA sequence alignments, which is based on combining two probabilistic graphical models: (1) a taxon graph (phylogenetic tree) representing the relationships among the taxa, and (2) a site graph (hidden Markov model) representing spatial correlations between nucleotides