PMID: 12775525May 31, 2003Paper

Accelerated likelihood surface exploration: the likelihood ratchet

Systematic Biology
R A Vos

Abstract

The existence of multiple likelihood maxima necessitates algorithms that explore a large part of the tree space. However, because of computational constraints, stepwise addition-based tree-searching methods do not allow for this exploration in reasonable time. Here, I present an algorithm that increases the speed at which the likelihood landscape can be explored. The iterative algorithm combines the computational speed of distance-based tree construction methods to arrive at approximations of the global optimum with the accuracy of optimality criterion based branch-swapping methods to improve on the result of the starting tree. The algorithm moves between local optima by iteratively perturbing the tree landscape through a process of reweighting randomly drawn samples of the underlying sequence data set. Tests on simulated and real data sets demonstrated that the optimal solution obtained using stepwise addition-based heuristic searches was found faster using the algorithm presented here. Tests on a previously published data set that established the presence of tree islands under maximum likelihood demonstrated that the algorithm identifies the same tree islands in a shorter amount of time than that needed using stepwise additio...Continue Reading

Citations

Nov 25, 2006·The Journal of Eukaryotic Microbiology·John C Clamp, Daniel Williams
Nov 6, 2014·Molecular Biology and Evolution·Lam-Tung NguyenBui Quang Minh
Jul 14, 2005·Systematic Biology·Nicolas SalaminVincent Savolainen Coates
Jun 8, 2007·The Journal of Eukaryotic Microbiology·Daniel Williams, John C Clamp
Apr 23, 2008·Proceedings. Biological Sciences·Diana M PercyRobert C Fleischer
Dec 9, 2008·International Journal of Systematic and Evolutionary Microbiology·Chen ShaoXiaofeng Lin
Oct 21, 2018·Applied and Environmental Microbiology·Haruhisa SugaMitsuro Hyakumachi
Jun 19, 2007·Mycological Research·Brian A PerryDonald H Pfister

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