Methodologies for Phylogenetic Inference
Anisimova, Maria (2015). Methodologies for Phylogenetic Inference. Encyclopedia of Life Sciences eLS: 1–5.. Peer reviewed.;
Phylogenetic inference from homologous molecular sequences is key to
hypothesis testing and problem solving not only in evolutionary biology but also
in a wide variety of other fields - from medicine to ecology. Model based
phylogenetic methods rely on Markov substitution models to describe the
molecular evolution as a stochastic process of character substitution over time on a phylogenetic tree relating the sequences. Model parameters are estimated with standard statistical inference methods, namely Bayesian and maximum likelihood approaches. A typical phylogenetic analysis first infers a multiple sequence alignment. Given this alignment, a phylogenetic tree is then estimated together with branch lengths and model parameters. Ideally, the alignment and phylogeny should be estimated simultaneously, amongst others to take alignment uncertainty into account.