Figure 1
From: Bayesian coestimation of phylogeny and sequence alignment
Alignments and homology structure. (Left:) Two alignments representing the same homology structure. A "homology structure" is defined as the set of all homology relationships between residues from the given sequences; residues are homologous if they appear in the same alignment column. Our recursion includes contributions from all alignments compatible with a given homology structure (itself represented by a single alignment). (Right:) Due to the evolutionary process acting on the sequences, homology relationships (arrows) will never 'cross' as depicted. This restriction on the equivalence relation ~ is codified by < h (see text).