Efficient estimation of the accuracy of the maximum likelihood method for ancestral state reconstruction
- 125 Downloads
The marginal maximum likelihood method is a widely-used method for ancestral state reconstruction. Given an evolution model (a phylogeny tree and the edge mutation rates) and the extant states (states on leaves), the method computes efficiently the most likely ancestral state on the root. However, when the extant states are randomly generated by using the evolutionary model, it is unknown how to efficiently calculate the expected reconstruction accuracy of the marginal maximum likelihood method. In this paper, a fully polynomial time approximation scheme (FPTAS) is presented for the calculation.
KeywordsAncestral state reconstruction Reconstruction accuracy Maximum likelihood method Polynomial time approximation
Unable to display preview. Download preview PDF.
- Farris JS (1983) The logical basis of phylogenetic analysis. In: Funk VA, Brooks DR (eds) Advances in cladistics. Botanical Garden, Bronx Google Scholar
- Felsenstein J (2004) Inferring Phylogenies. Sinauer Associates, Sunderland Google Scholar
- Li GL, Ma J, Zhang LX (2007) Selecting genomes for reconstruction of ancestral genomes. In: Durand D, Tesler G (eds) Proc RECOMB-CG 2007. LNCS, vol 4751. Springer, Berlin, pp 110–121 Google Scholar
- Maddison WP (1995) Calculating the probability distributions of ancestral states reconstructed by parsimony on phylogenetic trees. Syst Biol 44:474–481 Google Scholar
- Moossel (2007) Personal communication Google Scholar
- Pupko T, Peer I, Shamir R (2000) A fast algorithm for joint reconstruction of amino acid sequences. Mol Biol Evol 17:890–896 Google Scholar
- Yang ZH, Kumar S, Nei M (1995) A new method of inference of ancestral nucleotide and amino acid sequences. Genetics 141:1641–1650 Google Scholar