PhySortR

PhySortR processes phylogenetic trees as an R package to identify and classify clades, supporting detection of monophyletic relationships and reticulated evolution among taxa.

Key Features:

• Flexible Clade Identification: Identifies exclusive and non-exclusive clades based on tip labels, enabling focus on specified taxa without assuming tree rooting.
• Customizable Options: Provides parameters to evaluate clades within the context of the entire phylogenetic tree.
• Scalability and Efficiency: Processes thousands of simulated or empirical phylogenetic trees for large-scale phylogenomic analyses.
• Classification Outputs: Produces explicit classification results that specify clade membership and relationships relative to user-defined target taxa.

Scientific Applications:

• Phylogenomic screening: Screen large phylogenomic datasets to identify trees supporting specified monophyletic groups.
• Detection of reticulated evolution: Identify patterns indicative of reticulated evolution among taxa by classifying non-monophyletic or mixed clade patterns.
• Rooting-independent tree classification: Classify gene trees without prior assumptions about rooting to reduce bias in evolutionary inference.

Methodology:

Analyzes tip labels on phylogenetic trees to identify clades that unite target taxa and to distinguish exclusive versus non-exclusive clades; evaluates clades in the context of the whole tree without requiring a priori rooting assumptions and is implemented to process large numbers of trees efficiently.