A Comprehensive Protocol for Bayesian Phylogenetic Analysis Using MrBayes: From Sequence Alignment to Model Selection and Phylogenetic Inference
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 ri...
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| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Bio-protocol LLC
2025-04-01
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| Series: | Bio-Protocol |
| Online Access: | https://bio-protocol.org/en/bpdetail?id=5276&type=0 |
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| author | Jinxing Wang Fangmin Chen Xu Xiao Xinyao Yang Wanting Xia |
| author_facet | Jinxing Wang Fangmin Chen Xu Xiao Xinyao Yang Wanting Xia |
| author_sort | Jinxing Wang |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-d707514dcaac485391e98b2c6213f5f7 |
| institution | Kabale University |
| issn | 2331-8325 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | Bio-protocol LLC |
| record_format | Article |
| series | Bio-Protocol |
| spelling | doaj-art-d707514dcaac485391e98b2c6213f5f72025-08-20T03:48:46ZengBio-protocol LLCBio-Protocol2331-83252025-04-0115810.21769/BioProtoc.5276A Comprehensive Protocol for Bayesian Phylogenetic Analysis Using MrBayes: From Sequence Alignment to Model Selection and Phylogenetic InferenceJinxing Wang0Fangmin Chen1Xu Xiao2Xinyao Yang3Wanting Xia4Liaoning Province Key Laboratory of Urban Integrated Pest Management and Ecological Security, College of Life Science and Bioengineering, Shenyang University, Liaoning, ChinaLiaoning 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, ChinaSchool of Information Engineering, Wenzhou Business College, Wenzhou, Zhejiang, ChinaLiaoning 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, ChinaLiaoning 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, ChinaBayesian 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.https://bio-protocol.org/en/bpdetail?id=5276&type=0 |
| spellingShingle | Jinxing Wang Fangmin Chen Xu Xiao Xinyao Yang Wanting Xia A Comprehensive Protocol for Bayesian Phylogenetic Analysis Using MrBayes: From Sequence Alignment to Model Selection and Phylogenetic Inference Bio-Protocol |
| title | A Comprehensive Protocol for Bayesian Phylogenetic Analysis Using MrBayes: From Sequence Alignment to Model Selection and Phylogenetic Inference |
| title_full | A Comprehensive Protocol for Bayesian Phylogenetic Analysis Using MrBayes: From Sequence Alignment to Model Selection and Phylogenetic Inference |
| title_fullStr | A Comprehensive Protocol for Bayesian Phylogenetic Analysis Using MrBayes: From Sequence Alignment to Model Selection and Phylogenetic Inference |
| title_full_unstemmed | A Comprehensive Protocol for Bayesian Phylogenetic Analysis Using MrBayes: From Sequence Alignment to Model Selection and Phylogenetic Inference |
| title_short | A Comprehensive Protocol for Bayesian Phylogenetic Analysis Using MrBayes: From Sequence Alignment to Model Selection and Phylogenetic Inference |
| title_sort | comprehensive protocol for bayesian phylogenetic analysis using mrbayes from sequence alignment to model selection and phylogenetic inference |
| url | https://bio-protocol.org/en/bpdetail?id=5276&type=0 |
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