ipcoal

ipcoal simulates genealogies and DNA sequence data under the multispecies coalescent from species trees or networks to enable simulation and analysis of demographic scenarios including divergence times, effective population sizes, and migration.

Key Features:

• Coalescent simulation (themSprime): Generates genealogies and sequence data using the themSprime coalescent simulator from user-provided species trees or networks.
• Demographic model specification: Automates descriptions of complex demographic models including divergence times, effective population sizes, and migration events.
• Gene tree inference automation: Provides tools to automate inference of gene trees from simulated sequence data.
• Data output formats: Exports genealogies, sequences, and associated metadata in tabular formats for downstream analysis.
• Visualization capabilities: Includes visualization functions to inspect results and verify model behavior and accuracy.
• Posterior predictive analysis: Supports posterior predictive data analysis for assessing model fit and validating methods.

Scientific Applications:

• Methods validation: Produces controlled simulated datasets to validate coalescent-based inference methods.
• Demographic inference research: Enables exploration of how divergence, population size changes, and migration affect genealogical and sequence patterns.
• Teaching and learning: Serves as a resource for demonstrating coalescent theory and simulation-based analyses in evolutionary biology.

Methodology:

ipcoal leverages the themSprime simulator to generate genealogies and sequences from user-defined species trees or networks and automates complex demographic model descriptions under the multispecies coalescent.