TreeSample

TreeSample simulates phylogenetic trees from diverse evolutionary diversification models to produce unbiased tree shapes and branch lengths for evolutionary analyses.

Key Features:

• Model Compatibility: Supports a wide range of evolutionary diversification models applicable at species-level and higher taxonomic levels.
• Bias Mitigation: Addresses challenges associated with simple sampling approaches (SSA) that can produce systematically biased tree shapes or branch lengths by implementing alternative sampling strategies.
• General Sampling Approach (GSA): Implements a General Sampling Approach applicable to most evolutionary models to enhance reliability of simulated trees.
• Constant-Rate Birth-Death Model: Incorporates a specialized sampling approach for efficient and accurate generation of trees under constant-rate birth-death models.
• Bias Exploration and Correction: Includes methodologies to explore biases introduced by SSA, identify scenarios with pronounced bias, and ensure trait variance correlates appropriately with tree age.

Scientific Applications:

• Hypothesis Testing: Simulates phylogenetic trees under various evolutionary models to test hypotheses about species diversification and evolutionary processes.
• Comparative Analysis: Generates unbiased simulated trees for comparison with empirical phylogenetic data to assess model fit and evolutionary dynamics.

Methodology:

Uses rigorous mathematical methods and alternatives to SSA, explicitly including the General Sampling Approach (GSA) and specialized sampling procedures for constant-rate birth-death models.