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Two C++ libraries for counting trees on a phylogenetic terrace.

R Biczok1, P Bozsoky1, P Eisenmann1

  • 1Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany.

Bioinformatics (Oxford, England)
|May 11, 2018
PubMed
Summary

Phylogenetic tree inference software often misses terraces, which are groups of trees with identical likelihood scores. We developed efficient C++ tools to identify, count, and list trees on these terraces.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Phylogenetics

Background:

  • Phylogenetic tree space can contain 'terraces' – sets of distinct topologies with identical analytical likelihood scores.
  • Current phylogenetic inference software lacks efficient methods to detect, quantify, or enumerate trees on these terraces.

Purpose of the Study:

  • To address the lack of efficient computational tools for analyzing terraces in phylogenetic tree space.
  • To develop and implement algorithms for determining if a tree resides on a terrace, counting terrace trees, and enumerating all trees on a terrace.

Main Methods:

  • Developed two independent C++ implementations of the SUPERB algorithm for terrace analysis.
  • Utilized a bioinformatics programming contest format to foster efficient algorithm development.

Main Results:

  • The C++ implementations are over an order of magnitude faster and use an order of magnitude less memory than previous Python implementations.
  • Both C++ implementations produced identical results, ensuring reliability and accuracy.
  • The developed tools efficiently handle the counting and enumeration of trees on phylogenetic terraces.

Conclusions:

  • Efficient computational tools for analyzing phylogenetic terraces are now available.
  • These tools can be integrated into existing phylogenetic inference software to provide more comprehensive analyses.
  • The availability of these C++ implementations advances the study of phylogenetic tree space and likelihood landscapes.