Starless bias and parameter-estimation bias in the likelihood-based phylogenetic method.

ABSTRACT: I analyzed various site pattern combinations in a 4-OTU case to identify sources of starless bias and parameter-estimation bias in likelihood-based phylogenetic methods, and reported three significant contributions. First, the likelihood method is counterintuitive in that it may not generate a star tree with sequences that are equidistant from each other. This behaviour, dubbed starless bias, happens in a 4-OTU tree when there is an excess (i.e., more than expected from a star tree and a substitution model) of conflicting phylogenetic signals supporting the three resolved topologies equally. Special site pattern combinations leading to rejection of a star tree, when sequences are equidistant from each other, were identified. Second, fitting gamma distribution to model rate heterogeneity ov

SUBMITTER: Xia X 

PROVIDER: S-EPMC6690233 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature