An alternative approach to aligning alignments is to first infer ancestral sequences for each alignment, and then align the two ancestral sequences. Additionally, many algorithms based on the sum-of-pairs heuristic are complicated and slow, compared to pairwise alignment algorithms. However, the biological meaning of the sum-of-pairs of pairs heuristic is not obvious. Many popular alignment algorithms for DNA use the sum-of-pairs heuristic, where the score of a multiple alignment is the sum of its induced pairwise alignment scores. An important subproblem used by many multiple alignment approaches is that of aligning two multiple alignments. Ancestral sequence alignment under optimal conditionsĭirectory of Open Access Journals (Sweden)įull Text Available Abstract Background Multiple genome alignment is an important problem in bioinformatics.
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