A first order approximation of a joint Potts and phylogenetic model

Abstract

This study introduces a novel model that integrates the capacity of Potts models to capture structural dependencies with the computational efficiency afforded by Felsenstein's algorithm in phylogenetics. While the present work focuses on protein models, the PhyloPotts framework is equally applicable to alignments of discrete states, including RNA, DNA, and 3DI characters. Our findings indicate that, although phylogenetic estimates do not consistently exhibit reduced bias relative to standard models, the approach substantially enhances the accuracy of ancestral sequence reconstruction. The method is freely available via an open source implementation in the PhyloPotts package for BEAST 2 from https://github.com/rbouckaert/potts.