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).
Lunter et al. BMC Bioinformatics 2005 6:83 doi:10.1186/1471-2105-6-83