Incorporating alignment uncertainty into Felsenstein's phylogenetic bootstrap to improve its reliability.

ABSTRACT: Most evolutionary analyses are based on pre-estimated multiple sequence alignment. Wong et al. established the existence of an uncertainty induced by multiple sequence alignment when reconstructing phylogenies. They were able to show that in many cases different aligners produce different phylogenies, with no simple objective criterion sufficient to distinguish among these alternatives. We demonstrate that incorporating MSA induced uncertainty into bootstrap sampling can significantly increase correlation between clade correctness and its corresponding bootstrap value. Our procedure involves concatenating several alternative multiple sequence alignments of the same sequences, produced using different commonly used aligners. We then draw bootstrap replicates while favoring columns of the mo

SUBMITTER: Chang JM 

PROVIDER: S-EPMC8275982 | biostudies-literature | 2019 Feb

REPOSITORIES: biostudies-literature