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- Addario-Berry, L, et al.
(författare)
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Ancestral maximum likelihood of evolutionary trees is hard
- 2004
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Ingår i: Journal of Bioinformatics and Computational Biology. - 0219-7200 .- 1757-6334. ; 2:2, s. 257-271
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Tidskriftsartikel (refereegranskat)abstract
- Maximum likelihood (ML) (Felsenstein, 1981) is an increasingly popular optimality criterion for selecting evolutionary trees. Finding optimal ML trees appears to be a very hard computational task - in particular, algorithms and heuristics for ML take longer to run than algorithms and heuristics for maximum parsimony (MP). However, while MP has been known to be NP-complete for over 20 years, no such hardness result has been obtained so far for ML. In this work we make a first step in this direction by proving that ancestral maximum likelihood (AML) is NP-complete. The input to this problem is a set of aligned sequences of equal length and the goal is to find a tree and an assignment of ancestral sequences for all of that tree's internal vertices such that the likelihood of generating both the ancestral and contemporary sequences is maximized. Our NP-hardness proof follows that for MP given in (Day, Johnson and Sankoff, 1986) in that we use the same reduction from VERTEX COVER; however, the proof of correctness for this reduction relative to AML is different and substantially more involved.
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