phytools

phytools provides a wide range of methods for phylogenetic analysis, including visualization, manipulation, and inference of phylogenetic trees for phylogenetic comparative analysis.

Key Features:

• Trait Evolution Modeling: phytools includes functionality for fitting models of trait evolution.
• Ancestral State Reconstruction: phytools includes functionality for reconstructing ancestral states.
• Diversification Analysis: phytools includes functionality for studying diversification on trees.
• Phylogenetic Visualization: phytools includes functionality for visualizing phylogenies, comparative data, and fitted models.
• Phylogenetic Tree Manipulation: phytools provides methods for manipulation of phylogenetic trees.
• Phylogenetic Inference: phytools provides methods for inference of phylogenetic trees.

Scientific Applications:

• Phylogenetic Comparative Analysis: phytools is utilized for phylogenetic comparative analysis using an estimated phylogenetic tree or set of trees to make secondary inferences.
• Trait Evolution Inference: phytools enables secondary inferences about trait evolution.
• Diversification Dynamics: phytools enables secondary inferences about diversification dynamics.
• Biogeography: phytools enables secondary inferences about biogeography.
• Community Ecology: phytools enables secondary inferences about community ecology.

Methodology:

phytools is implemented as an R package consisting of hundreds of different functions covering a variety of methods and purposes in phylogenetic biology.