Print Email Facebook Twitter On computing the maximum parsimony score of a phylogenetic network Title On computing the maximum parsimony score of a phylogenetic network Author Fischer, M. Van Iersel, L.J.J. Kelk, S. Scornavacca, C. Faculty Electrical Engineering, Mathematics and Computer Science Department Electrical Sustainable Energy Date 2015-12-31 Abstract Phylogenetic networks are used to display the relationship among different species whose evolution is not treelike, which is the case, for instance, in the presence of hybridization events or horizontal gene transfers. Tree inference methods such as maximum parsimony need to be modified in order to be applicable to networks. In this paper, we discuss two different definitions of maximum parsimony on networks, “hardwired” and “softwired,” and examine the complexity of computing them given a network topology and a character. By exploiting a link with the problem Multiterminal Cut, we show that computing the hardwired parsimony score for 2-state characters is polynomial-time solvable, while for characters with more states this problem becomes NP-hard but is still approximable and fixed parameter tractable in the parsimony score. On the other hand we show that, for the softwired definition, obtaining even weak approximation guarantees is already difficult for binary characters and restricted network topologies, and fixed-parameter tractable algorithms in the parsimony score are unlikely. On the positive side we show that computing the softwired parsimony score is fixed-parameter tractable in the level of the network, a natural parameter describing how tangled reticulate activity is in the network. Finally, we show that both the hardwired and the softwired parsimony scores can be computed efficiently using integer linear programming. The software has been made freely available Subject phylogenetic treesphylogenetic networksparsimonycomplexityapproximabilityfixed-parameter tractabilitysoftware To reference this document use: http://resolver.tudelft.nl/uuid:67575ea8-bcde-494a-82a7-005f17f9b5f9 Publisher SIAM ISSN 0895-4801 Source SIAM Journal on Discrete Mathematics, 29(1)2015 Part of collection Institutional Repository Document type journal article Rights (c) 2015 The Authors and SIAM Files PDF 322848.pdf 437.4 KB Close viewer /islandora/object/uuid:67575ea8-bcde-494a-82a7-005f17f9b5f9/datastream/OBJ/view