A Comprehensive Protocol for Bayesian Phylogenetic Analysis Using MrBayes: From Sequence Alignment to Model Selection and Phylogenetic Inference
Jinxing Wang,
Fangmin Chen,
Xu Xiao,
Xinyao Yang,
Wanting Xia
Affiliations
Jinxing Wang
Liaoning Province Key Laboratory of Urban Integrated Pest Management and Ecological Security, College of Life Science and Bioengineering, Shenyang University, Liaoning, China
Fangmin Chen
Liaoning Province Key Laboratory of Urban Integrated Pest Management and Ecological Security, College of Life Science and Bioengineering, Shenyang University, Liaoning, ChinaKey Laboratory of Ecological Restoration of Regional Contaminated Environment, Ministry of Education, Shenyang University, Shenyang, Liaoning, China
Xu Xiao
School of Information Engineering, Wenzhou Business College, Wenzhou, Zhejiang, China
Xinyao Yang
Liaoning Province Key Laboratory of Urban Integrated Pest Management and Ecological Security, College of Life Science and Bioengineering, Shenyang University, Liaoning, ChinaKey Laboratory of Ecological Restoration of Regional Contaminated Environment, Ministry of Education, Shenyang University, Shenyang, Liaoning, China
Wanting Xia
Liaoning Province Key Laboratory of Urban Integrated Pest Management and Ecological Security, College of Life Science and Bioengineering, Shenyang University, Liaoning, ChinaKey Laboratory of Ecological Restoration of Regional Contaminated Environment, Ministry of Education, Shenyang University, Shenyang, Liaoning, China
Bayesian phylogenetic analysis is essential for elucidating evolutionary relationships among organisms. Traditional methods often rely on fixed models and manual parameter settings, which can limit accuracy and efficiency. This protocol presents an integrated workflow that leverages GUIDANCE2 for rigorous sequence alignment, ProtTest and MrModeltest for robust model selection, and MrBayes for phylogenetic tree estimation through Bayesian inference. By automating key steps and providing detailed command-line instructions, this protocol enhances the reliability and reproducibility of phylogenetic studies.
