Phylogenetics - Construction of A Phylogenetic Tree

Construction of A Phylogenetic Tree

The scientific methods of phylogenetics are often grouped under the term cladistics. The most common ones are parsimony, maximum likelihood, and MCMC-based Bayesian inference. All methods depend upon an implicit or explicit mathematical model describing the evolution of characters observed in the species included; all can be, and are, used for molecular data, wherein the characters are aligned nucleotide or amino acid sequences, and all but maximum likelihood (see below) can be, and are, used for morphological data.

Phenetics, popular in the mid-20th century but now largely obsolete, uses distance matrix-based methods to construct trees based on overall similarity, which is often assumed to approximate phylogenetic relationships.