Multiple maxima of likelihood in phylogenetic trees: An analytic approach

Benny Chor*, Michael D. Hendy, Barbara R. Holland, David Penny

*Corresponding author for this work

Research output: Contribution to conferencePaperpeer-review

Abstract

Maximum likelihood (ML) is a widely used criterion for selecting optimal evolutionary trees. However, little is known on the nature of the likelihood surface for trees, especially as to the frequency of multiple optima. We initiate an analytic study for identifying sequences that generate multiple optima. We report a new approach to calculating ML directly, which we have used to find large families of sequences that have multiple optima, including sequences with a continuum of optimal points. Such datasets are best supported by different (two or more) phylogenies that vary significantly in their timings of evolutionary events. Some standard biological processes can lead to data with multiple optima and consequently the field needs further investigation. Our results imply that hill climbing techniques, as currently implemented in various software packages, cannot guarantee to find the global ML point, even if it is unique.

Original languageEnglish
Pages108-117
Number of pages10
StatePublished - 2000
Externally publishedYes
EventRECOMB 2000: 4th Annual International Conference on Computational Molecular Biology - Tokyo, Jpn
Duration: 8 Apr 200011 Apr 2000

Conference

ConferenceRECOMB 2000: 4th Annual International Conference on Computational Molecular Biology
CityTokyo, Jpn
Period8/04/0011/04/00

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