期刊
MOLECULAR BIOLOGY AND EVOLUTION
卷 36, 期 11, 页码 2620-2628出版社
OXFORD UNIV PRESS
DOI: 10.1093/molbev/msz172
关键词
BEAST; Skygrid; coalescent; Bayesian phylogenetics; pathogen phylodynamics; TempEst; Tracer
资金
- Biotechnology and Biological Sciences Research Council (BBSRC) [BB/M010996/1]
- Interne Fondsen KU Leuven/Internal Funds KU Leuven [C14/18/094]
- Wellcome Trust [206298/Z/17/Z]
- European Union Seventh Framework Programme for research, technological development, and demonstration [725422-RESERVOIRDOCS]
- BBSRC [1950353] Funding Source: UKRI
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.
作者
我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。
推荐
暂无数据