Finding agreement cherry-reduced subnetworks in level-1 networks
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Phylogenetic networks are increasingly being considered as better suited to represent the complexity of the evolutionary relationships between species. One class of phylogenetic networks that has received a lot of attention recently is the class of orchard networks, which is composed of networks that can be reduced to a single leaf using cherry reductions. Cherry reductions, also called cherry-picking operations, remove either a leaf of a simple cherry (sibling leaves sharing a parent) or a reticulate edge of a reticulate cherry (two leaves whose parents are connected by a reticulate edge). In this paper, we present a fixed-parameter tractable algorithm to solve the problem of finding a maximum agreement cherry-reduced subnetwork (MACRS) between two rooted binary level-1 networks. This is first exact algorithm proposed to solve the MACRS problem. As proven in earlier work, there is a direct relationship between finding an MACRS and calculating a distance based on cherry operations. As a result, the proposed algorithm also provides a distance that can be used for the comparison of level-1 networks.
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