QMaker: Fast and Accurate Method to Estimate Empirical Models of Protein Evolution.

ABSTRACT: Amino acid substitution models play a crucial role in phylogenetic analyses. Maximum likelihood (ML) methods have been proposed to estimate amino acid substitution models; however, they are typically complicated and slow. In this article, we propose QMaker, a new ML method to estimate a general time-reversible $Q$ matrix from a large protein data set consisting of multiple sequence alignments. QMaker combines an efficient ML tree search algorithm, a model selection for handling the model heterogeneity among alignments, and the consideration of rate mixture models among sites. We provide QMaker as a user-friendly function in the IQ-TREE software package (http://www.iqtree.org) supporting the use of multiple CPU cores so that biologists can easily estimate amino acid substitution models from

SUBMITTER: Minh BQ 

PROVIDER: S-EPMC8357343 | biostudies-literature | 2021 Aug

REPOSITORIES: biostudies-literature