Efficient inference, potential, and limitations of site-specific substitution models.

ABSTRACT: Natural selection imposes a complex filter on which variants persist in a population resulting in evolutionary patterns that vary greatly along the genome. Some sites evolve close to neutrally, while others are highly conserved, allow only specific states, or only change in concert with other sites. On one hand, such constraints on sequence evolution can be to infer biological function, one the other hand they need to be accounted for in phylogenetic reconstruction. Phylogenetic models often account for this complexity by partitioning sites into a small number of discrete classes with different rates and/or state preferences. Appropriate model complexity is typically determined by model selection procedures. Here, we present an efficient algorithm to estimate more complex models that allow

SUBMITTER: Puller V 

PROVIDER: S-EPMC7733610 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature