Figure 1.

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
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