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- Title
Characterizing Local Optima for Maximum Parsimony.
- Authors
Urheim, Ellen; Ford, Eric; St. John, Katherine
- Abstract
Finding the best phylogenetic tree under the maximum parsimony optimality criterion is computationally difficult. We quantify the occurrence of such optima for well-behaved sets of data. When nearest neighbor interchange operations are used, multiple local optima can occur even for 'perfect' sequence data, which results in hill-climbing searches that never reach a global optimum. In contrast, we show that when neighbors are defined via the subtree prune and regraft metric, there is a single local optimum for perfect sequence data, and thus, every such search finds a global optimum quickly. We further characterize conditions for which sequences simulated under the Cavender-Farris-Neyman and Jukes-Cantor models of evolution yield well-behaved search spaces.
- Subjects
PARSIMONIOUS models; PHYLOGENY; BIG data; PRUNE; WEBOMETRICS
- Publication
Bulletin of Mathematical Biology, 2016, Vol 78, Issue 5, p1058
- ISSN
0092-8240
- Publication type
Article
- DOI
10.1007/s11538-016-0174-0