Abstract
. Many biological systems involve the dynamics of interacting evolutionary units . Species and genome evolution . Host and symbiont coevolution . A cophylogeny consists of two phylogenetic trees and a mapping between them that can be explained by a sequence of biological events . Want to use Bayesian inference to reconstruct cophylogenies from sequence data . Existing methods assume that the host’s evolutionary history is known exactly . Need a general framework for inference with arbitrarily complex cophylogeny models
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