NQMaker: Estimating Time Nonreversible Amino Acid Substitution Models.

ABSTRACT: Amino acid substitution models are a key component in phylogenetic analyses of protein sequences. All commonly used amino acid models available to date are time-reversible, an assumption designed for computational convenience but not for biological reality. Another significant downside to time-reversible models is that they do not allow inference of rooted trees without outgroups. In this article, we introduce a maximum likelihood approach nQMaker, an extension of the recently published QMaker method, that allows the estimation of time nonreversible amino acid substitution models and rooted phylogenetic trees from a set of protein sequence alignments. We show that the nonreversible models estimated with nQMaker are a much better fit to empirical alignments than pre-existing reversible mode

SUBMITTER: Dang CC 

PROVIDER: S-EPMC9366462 | biostudies-literature | 2022 Aug

REPOSITORIES: biostudies-literature