Perfect phylogeny

Perfect phylogeny is a term used in computational phylogenetics to denote a phylogenetic tree in which all internal nodes may be labeled such that all characters evolve down the tree without homoplasy. That is, characteristics do not hold to evolutionary convergence, and do not have analogous structures. Statistically, this can be represented as an ancestor having state '0' in all characteristics where 0 represents a lack of that characteristic. Each of these characteristics changes from 0 to 1 exactly once and never reverts to state 0. It is rare that actual data adheres to the concept of perfect phylogeny.A perfect phylogeny for an n x m character state matrix M is a rooted tree T with n leaves satisfying:An example of a character matrix that can be depicted as a perfect phylogeny Perfect phylogeny is a term used in computational phylogenetics to denote a phylogenetic tree in which all internal nodes may be labeled such that all characters evolve down the tree without homoplasy. That is, characteristics do not hold to evolutionary convergence, and do not have analogous structures. Statistically, this can be represented as an ancestor having state '0' in all characteristics where 0 represents a lack of that characteristic. Each of these characteristics changes from 0 to 1 exactly once and never reverts to state 0. It is rare that actual data adheres to the concept of perfect phylogeny. In general there are two different data types that are used in the construction of a phylogenetic tree. In distance-based computations a phylogenetic tree is created by analyzing relationships among the distance between species and the edge lengths of a corresponding tree. Using a character-based approach employs character states across species as an input in an attempt to find the most 'perfect' phylogenetic tree. The statistical components of a perfect phylogenetic tree can best be described as follows: