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.
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