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Updated: Jun 27, 2026
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A Practical Guide to Phylogenetics for Nonexperts
Published on: February 5, 2014
phyloPipeR: An R Package for End-to-End Phylogenetic Reconstruction and Tree Comparison
Feifei Li1, Yue Zou1, Tong Li1
1Computational and Integrative Biology Group, College of Life Sciences, Chongqing Normal University, Chongqing 401331, China.
Current Issues in Molecular Biology
|June 26, 2026
Summary
This study introduces phyloPipeR, an R package for automated phylogenetic analysis. It streamlines complex workflows from sequence retrieval to tree comparison, enhancing reproducibility and accessibility for evolutionary studies.
Area of Science:
- Evolutionary biology
- Bioinformatics
- Computational phylogenetics
Background:
- Phylogenetic reconstruction involves multiple complex, independent tools, hindering reproducibility.
- Large-scale phylogenetic analyses face significant technical challenges and reproducibility issues.
Purpose of the Study:
- To present phyloPipeR, an R package offering an integrated, automated framework for phylogenetic analysis.
- To simplify and enhance the reproducibility of end-to-end phylogenetic workflows.
Main Methods:
- Developed an R package, phyloPipeR, for automated phylogenetic analysis.
- Integrated ortholog retrieval, sequence alignment, trimming, tree inference, and tree comparison.
- Supported modular execution of individual workflow steps.
Main Results:
- phyloPipeR provides a unified environment for complete phylogenetic workflows.
- The package implements diverse phylogenetic inference methods and strategies (concatenation, coalescent).
- Facilitates quantitative tree comparison within the same framework.
Conclusions:
- phyloPipeR reduces technical barriers and improves reproducibility in phylogenetic analyses.
- Offers a scalable solution for systematic and integrative evolutionary studies.
- Enhances accessibility for researchers conducting phylogenetic reconstruction.
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