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Coala: an R framework for coalescent simulation.

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  • 1Department of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried 82152, Germany.

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Summary
This summary is machine-generated.

Coalescent simulation programs generate genetic data for evolutionary models. The R package coala unifies syntax for multiple simulators, enhancing biological realism in genetic data generation.

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Area of Science:

  • Population genetics
  • Computational biology
  • Evolutionary genetics

Background:

  • Coalescent theory is fundamental for simulating genetic data under evolutionary models.
  • Existing coalescent simulators often require different syntaxes, hindering workflow integration.
  • Generating realistic genetic datasets is crucial for population genetic inference.

Purpose of the Study:

  • To introduce coala, an R package designed to unify the interface for various coalescent simulation programs.
  • To facilitate the execution of simulations, calculation of summary statistics, and combination of simulation outputs.
  • To enable the creation of more biologically realistic genetic data for research.

Main Methods:

  • Development of an R package named coala.
  • Implementation of a unified syntax for calling multiple coalescent simulation backends.
  • Integration of functions for calculating summary statistics and combining simulation results.

Main Results:

  • coala provides a consistent interface to diverse coalescent simulators.
  • The package allows for the computation of additional summary statistics beyond basic simulation output.
  • Multiple simulations can be combined to generate complex, biologically realistic datasets.

Conclusions:

  • coala simplifies and standardizes the use of coalescent simulations in R.
  • The package enhances the ability to generate sophisticated genetic data for evolutionary studies.
  • coala is publicly available on CRAN and GitHub, promoting accessibility and reproducibility.