Affiliation:
1. Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
2. Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
Abstract
Abstract
Inferring past population dynamics over time from heterochronous molecular sequence data is often achieved using the Bayesian Skygrid model, a nonparametric coalescent model that estimates the effective population size over time. Available in BEAST, a cross-platform program for Bayesian analysis of molecular sequences using Markov chain Monte Carlo, this coalescent model is often estimated in conjunction with a molecular clock model to produce time-stamped phylogenetic trees. We here provide a practical guide to using BEAST and its accompanying applications for the purpose of drawing inference under these models. We focus on best practices, potential pitfalls, and recommendations that can be generalized to other software packages for Bayesian inference. This protocol shows how to use TempEst, BEAUti, and BEAST 1.10 (http://beast.community/; last accessed July 29, 2019), LogCombiner as well as Tracer in a complete workflow.
Funder
Biotechnology and Biological Sciences Research Council
Publisher
Oxford University Press (OUP)
Subject
Genetics,Molecular Biology,Ecology, Evolution, Behavior and Systematics
Cited by
118 articles.
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