Gradients Do Grow on Trees: A Linear-Time O(N)-Dimensional Gradient for Statistical Phylogenetics

Calculation of the log-likelihood stands as the computational bottleneck for many statistical phylogenetic algorithms. Even worse is its gradient evaluation, often used to target regions of high probability. Order O(N)-dimensional gradient calculations based on the standard pruning algorithm require...

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Bibliographic Details
Published in:	Molecular biology and evolution Vol. 37; no. 10; pp. 3047 - 3060
Main Authors:	Ji, Xiang, Zhang, Zhenyu, Holbrook, Andrew, Nishimura, Akihiko, Baele, Guy, Rambaut, Andrew, Lemey, Philippe, Suchard, Marc A
Format:	Journal Article
Language:	English
Published:	United States Oxford University Press 01.10.2020
Subjects:	Algorithms Bayesian analysis Computer applications Dengue fever Evolution, Molecular Flavivirus - genetics Heterogeneity Inference Lassa virus - genetics Markov processes Methods Models, Genetic Next-generation sequencing Phylogenetics Phylogeny Process parameters Sequences Statistical analysis Statistics Vector-borne diseases Viruses West Nile virus linear-time gradient algorithm random-effects molecular clock model Bayesian inference maximum likelihood
ISSN:	0737-4038, 1537-1719, 1537-1719
Online Access:	Get full text
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