PhySortR: a fast, flexible tool for sorting phylogenetic trees in R.

Area of Science:

• Phylogenetics and evolutionary biology
• Bioinformatics and computational biology

Background:

• Interpreting large phylogenomic datasets, especially screening thousands of phylogenetic trees, presents a significant bottleneck.
• Identifying specific clades (groups of taxa) within these trees is crucial for understanding evolutionary relationships, including monophyly and reticulated evolution.

Purpose of the Study:

• To introduce PhySortR, a fast and flexible R package designed for classifying phylogenetic trees.
• To enable efficient identification of both exclusive and non-exclusive clades based on tip labels.
• To provide customizable options for assessing clades within the broader tree context.

Main Methods:

• Development of PhySortR, an R package functioning as a command-line tool.
• Utilizing tip labels to identify clades uniting target taxa.
• Implementing customizable options for clade assessment relative to the entire tree structure.
• Testing scalability and performance using simulated and empirical phylogenomic datasets.

Main Results:

• PhySortR demonstrates efficient classification of thousands of phylogenetic trees.
• The package successfully identifies target clades without requiring a priori tree rooting.
• PhySortR yields readily interpretable trees that clearly satisfy user queries.
• The tool is shown to be scalable and automatable for large-scale analyses.

Conclusions:

• PhySortR significantly accelerates the interpretation of phylogenomic data by automating tree classification.
• The package offers a flexible and powerful solution for identifying specific evolutionary groupings within large tree sets.
• PhySortR enhances the process of inferring evolutionary history from complex phylogenomic outputs.