Phylogenetic Trees and Multiple Alignments

Character-based methods for Phylogeny Construction

A character c is compatible with a tree T, if the set of all nodes with the state s of c form a subtree (a connected subgraph) of T.

If all given characters are compatible to a phylogenetic tree, the tree represents a Perfect Phylogeny.

If two characters are implementable for the same tree, the characters are compatible. A set of binary characters being pairwise compatible forms a perfect phylogeny, that is not true in general.

Real data usually don't support a perfect phylogeny. A relaxation of the perfect phylogny problem is the parsimonious tree problem.