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Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

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A Comprehensive Protocol for Bayesian Phylogenetic Analysis Using MrBayes: From Sequence Alignment to Model Selection

Jinxing Wang¹, Fangmin Chen^1,2, Xu Xiao³

¹Liaoning Province Key Laboratory of Urban Integrated Pest Management and Ecological Security, College of Life Science and Bioengineering, Shenyang University, Liaoning, China.

|April 28, 2025

Summary

This study introduces an automated workflow for Bayesian phylogenetic analysis, improving accuracy and reproducibility in evolutionary studies. It integrates tools for sequence alignment, model selection, and tree estimation, simplifying complex analyses.

Keywords:

Bayesian phylogenetic analysis Evolutionary model selection GUIDANCE2 MAFFT MrBayes MrModeltest ProtTest Sequence alignment

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Last Updated: May 10, 2025

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

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Published on: August 16, 2017

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

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Published on: August 14, 2018

A Practical Guide to Phylogenetics for Nonexperts

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Published on: February 5, 2014

Area of Science:

Evolutionary Biology
Bioinformatics

Background:

Bayesian phylogenetic analysis is crucial for understanding evolutionary relationships.
Conventional methods often require manual parameter tuning and fixed models, potentially compromising accuracy and efficiency.

Purpose of the Study:

To present an integrated, automated workflow for Bayesian phylogenetic analysis.
To enhance the reliability and reproducibility of evolutionary relationship studies.

Main Methods:

Utilized GUIDANCE2 for sequence alignment, combined with MAFFT for handling complex evolutionary events.
Employed ProtTest and MrModeltest for automated selection of protein and nucleotide substitution models, respectively.
Integrated MrBayes for phylogenetic tree estimation via Bayesian inference, providing command-line instructions.

Main Results:

The workflow automates critical steps in phylogenetic analysis, from alignment to tree estimation.
Demonstrated enhanced reliability and reproducibility in phylogenetic studies through an integrated approach.
Successfully combined specialized tools (GUIDANCE2, ProtTest, MrModeltest, MrBayes) into a cohesive protocol.

Conclusions:

The presented protocol offers a streamlined and robust method for Bayesian phylogenetic analysis.
Automation of key steps significantly improves the efficiency and accuracy of evolutionary relationship elucidation.
This integrated workflow serves as a valuable resource for researchers in evolutionary biology and bioinformatics.