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A Practical Guide to Phylogenetics for Nonexperts
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PhylogeneticGraph (PhyG) a new phylogenetic graph search and optimization program.

Ward C Wheeler1, Alexander Washburn2, Louise M Crowley1

  • 1Division of Invertebrate Zoology, American Museum of Natural History, 200 Central Park West, New York, NY, 10024, USA.

Cladistics : the International Journal of the Willi Hennig Society
|October 19, 2023
PubMed
Summary
This summary is machine-generated.

Phylogenetic Graph (PhyG) is a new open-source tool for analyzing diverse phylogenetic data, including complex networks beyond trees. It improves upon previous methods for faster and more optimal evolutionary analyses.

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Area of Science:

  • Computational Biology
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Phylogenetic analysis traditionally focuses on tree structures, limiting the study of complex evolutionary events.
  • Existing tools often struggle with diverse data types and network structures, hindering comprehensive evolutionary research.

Purpose of the Study:

  • Introduce Phylogenetic Graph (PhyG), an open-source software for advanced phylogenetic analyses.
  • Enable the analysis of diverse data types and network structures, including softwired and hardwired networks, alongside traditional trees.
  • Enhance heuristic optimality and execution speed for phylogenetic tree alignment and search.

Main Methods:

  • PhyG integrates novel graph construction and refinement algorithms.
  • Supports a wide range of input data, including qualitative and sequence data with numerous character states.
  • Implements parsimony and No-Common-Mechanism Likelihood optimization methods.

Main Results:

  • PhyG demonstrates significant improvements in heuristic optimality (up to 7%) compared to previous tools like POY5.
  • Achieves substantial reductions in execution time (up to 200-fold) for combined data tree-alignment.
  • Facilitates the analysis of complex evolutionary scenarios such as horizontal gene transfer and hybridization.

Conclusions:

  • PhyG provides a powerful and versatile platform for phylogenetic inference, accommodating diverse data and evolutionary models.
  • The tool's enhancements in performance and data handling capabilities advance the field of computational evolutionary biology.
  • PhyG is poised to become an essential resource for researchers investigating complex evolutionary histories.