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RAxML Grove: an empirical phylogenetic tree database.

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  • 1Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany.

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Summary
This summary is machine-generated.

RAxML Grove is a new database of over 60,000 phylogenetic trees and model parameters from empirical data. It aids in generating realistic simulations for phylogenetic model assessment.

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Area of Science:

  • Computational Biology
  • Phylogenetics
  • Bioinformatics

Background:

  • Assessing new phylogenetic models requires realistic simulated data.
  • Current methods for generating synthetic phylogenetic data lack appropriate parameter distributions and tree shapes reflective of empirical data.

Purpose of the Study:

  • To introduce RAxML Grove, a database of empirical phylogenetic trees and model parameters.
  • To provide a resource for improving the realism of simulated data for phylogenetic model evaluation.

Main Methods:

  • Compiled over 60,000 inferred phylogenetic trees and model parameters.
  • Utilized anonymized empirical datasets analyzed with RAxML and RAxML-NG on web servers.
  • Developed two applications to demonstrate the database's utility.

Main Results:

  • Established RAxML Grove, a comprehensive database of empirical phylogenetic data.
  • Demonstrated the utility of RAxML Grove for designing realistic simulation studies.
  • Highlighted the value of analyzing empirical model parameter and tree shape distributions.

Conclusions:

  • RAxML Grove offers a valuable resource for the phylogenetic community.
  • The database facilitates more accurate simulation studies for phylogenetic model development.
  • RAxML Grove aids in understanding empirical data distributions for improved phylogenetic inference.