Skip to Main content Skip to Navigation
Journal articles

On Computing the Maximum Parsimony Score of a Phylogenetic Network

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.
Document type :
Journal articles
Complete list of metadata

Cited literature [32 references]  Display  Hide  Download

https://hal.archives-ouvertes.fr/hal-02154929
Contributor : Celine Scornavacca Connect in order to contact the contributor
Submitted on : Wednesday, December 18, 2019 - 3:35:10 PM
Last modification on : Thursday, October 14, 2021 - 12:06:10 PM
Long-term archiving on: : Thursday, March 19, 2020 - 9:48:19 PM

File

Scornavacca_03.pdf
Publisher files allowed on an open archive

Identifiers

Collections

Citation

Mareike Fischer, Leo van Iersel, Steven Kelk, Celine Scornavacca. On Computing the Maximum Parsimony Score of a Phylogenetic Network. SIAM Journal on Discrete Mathematics, Society for Industrial and Applied Mathematics, 2015, 29 (1), pp.559-585. ⟨10.1137/140959948⟩. ⟨hal-02154929⟩

Share

Metrics

Record views

362

Files downloads

265