Landry K, Tremblay-Savard O, Lafond M. A Fixed-Parameter Tractable Algorithm for Finding Agreement Cherry-Reduced Subnetworks in Level-1 Orchard Networks.
J Comput Biol 2024;
31:360-379. [PMID:
38117611 DOI:
10.1089/cmb.2023.0317]
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Abstract
Phylogenetic networks are increasingly being considered better suited to represent the complexity of the evolutionary relationships between species. One class of phylogenetic networks that have 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 article, 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 the first exact algorithm proposed to solve the MACRS problem. As proven in an 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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