Compatibility of phylogenetic trees is the most important concept underlying
widely-used methods for assessing the agreement of different phylogenetic trees
with overlapping taxa and combining them into common supertrees to reveal the
tree of life. The notion of ancestral compatibility of phylogenetic trees with
nested taxa was introduced by Semple et al in 2004. In this paper we analyze in
detail the meaning of this compatibility from the points of view of the local
structure of the trees, of the existence of embeddings into a common supertree,
and of the joint properties of their cluster representations. Our analysis
leads to a very simple polynomial-time algorithm for testing this
compatibility, which we have implemented and is freely available for download
from the BioPerl collection of Perl modules for computational biology.Comment: Submitte
