An independent base composition of each rate class for improved likelihood-based phylogeny estimation; the 5rf model.

ABSTRACT: The combination of a time reversible Markov process with a "hidden" mixture of gamma distributed relative site rates plus invariant sites have become the most favoured options for likelihood and other probabilistic models of nucleotide evolution (e.g., tr4gi which approximates a gamma with four rate classes). However, these models assume a homogeneous and stationary distribution of nucleotide (character or base) frequencies. Here, we explore the potential benefits and pitfalls of allowing each rate category (rate class) of a 4gi mixture model to have its own base frequencies. This is achieved by starting each of the five rate classes, at the tree's root, with its own free choice of nucleotide frequencies to create a 4gi5rf model or a 5rf model in s

SUBMITTER: Waddell PJ 

PROVIDER: S-EPMC11398347 | biostudies-literature | 2024 Sep

REPOSITORIES: biostudies-literature