Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies

By Andrew Rambaut. Bioinform., 2000

377 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Public Health, Environmental and Occupational Health

View Paper: https://www.semanticscholar.org/paper/61971052682632a90d316de256dc377b55ade629

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Citations in the corpus

Fast Dating Using Least-Squares Criteria and Algorithms (2015, methodology): “Maximum-likelihood methods have also been designed to deal with simpler models (Rambaut 2000).”
Phylogenetic Analysis by Maximum Likelihood (PAML) (2002, methodology): “This is used for testing the TipDate models of Rambaut (2000).”
Circulation of genetically distinct contemporary human coronavirus OC43 strains (2005, neutral): “The molecular clock hypothesis was tested using a likelihood ratio test that evaluates the relative goodness-of-fit of a model assuming a molecular clock for serially-sampled data compared to a model that does not assume rate constancy (Rambaut, 2000).”
Relaxed Phylogenetics and Dating with Confidence (2006, background): “Calibration information for the rate of evolution stems from the fact that each sequence has a date of sampling associated with it [29].”
Origin and evolution of influenza virus hemagglutinin genes. (2002, background): “Also, the molecular clock was not rejected at the 1% significance level for the phylogenetic tree in figure 5 by the likelihoodratio test (Rambaut 2000; Yang 2000) but was rejected for the tree in figure 2c.”
Complete Genomic Sequence of Human Coronavirus OC43: Molecular Clock Analysis Suggests a Relatively Recent Zoonotic Coronavirus Transmission Event (2005, methodology): “Evolutionary rates and divergence times were estimated by using maximum likelihood in the TipDate software package, version 1.2 ( 49 ), and Bayesian inference in BEAST, version 1.03 (kindly made available by A. J. Drummond and A. Rambaut, University of Oxford; http: //evolve.zoo.ox.ac.uk/beast/).”
TreeTime: Maximum-likelihood phylodynamic analysis (2017, methodology): “The molecular clock has since been used to date the divergence of ancient proteins billions of years ago as well as the spread of RNA viruses on time scales less than a year (Langley and Fitch, 1974; Rambaut, 2000; Sanderson, 2003; Yoder and Yang, 2000).”
Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty. (2012, background): “…the curve values are given at the bottom right of each plot. alternative to the likelihood ratio test that conditions on a single tree topology to test whether including the sampling dates in a dated-tip model significantly improves the fit of the clock models (Rambaut 2000; Suchard et al. 2003).”
Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen) (2016, neutral): “Time-scaled trees can be estimated using many statistical approaches, including Bayesian inference (e.g., Drummond et al. 2012), maximum likelihood (e.g., Rambaut 2000; Sanderson 2003; Yang 2007), or heuristic methods (e.g., Drummond and Rodrigo 2000).”
Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times. (2009, background): “…nodes (i.e., the tips or leaves of the tree) are only possible when the analysis involves heterochronous sequence data, such as those from serially sampled viruses or ancient DNA (Rambaut 2000), or when dated fossils are included in an analysis involving morphological characters (Lee et al. 2009).”
Rates of Molecular Evolution in RNA Viruses: A Quantitative Phylogenetic Analysis (2002, methodology): “Our analytical method requires as input data viruses from which samples of sequences have been isolated at different times (Rambaut 2000).”