GTRpmix: A Linked General Time-Reversible Model for Profile Mixture Models.

ABSTRACT: Profile mixture models capture distinct biochemical constraints on the amino acid substitution process at different sites in proteins. These models feature a mixture of time-reversible models with a common matrix of exchangeabilities and distinct sets of equilibrium amino acid frequencies known as profiles. Combining the exchangeability matrix with each profile generates the matrix of instantaneous rates of amino acid exchange for that profile. Currently, empirically estimated exchangeability matrices (e.g. the LG matrix) are widely used for phylogenetic inference under profile mixture models. However, these were estimated using a single profile and are unlikely optimal for profile mixture models. Here, we describe the GTRpmix model that allows maximum likelihood estimation of a common exc

SUBMITTER: Banos H 

PROVIDER: S-EPMC11371462 | biostudies-literature | 2024 Sep

REPOSITORIES: biostudies-literature