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MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation.

Diep Thi Hoang1, Le Sy Vinh1, Tomáš Flouri2

  • 1University of Engineering and Technology, Vietnam National University, Hanoi, Vietnam.

BMC Evolutionary Biology
|February 3, 2018
PubMed
Summary
This summary is machine-generated.

MPBoot accelerates phylogenetic tree branch support calculations for maximum parsimony. This ultrafast bootstrap approximation offers significant speedups and more accurate results compared to existing methods.

Keywords:
Maximum parsimonyNonparametric bootstrapPhylogenetic inference

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Area of Science:

  • Computational Biology
  • Phylogenetics
  • Bioinformatics

Background:

  • Nonparametric bootstrap is standard for phylogenetic tree branch support.
  • Bootstrapping is computationally intensive, creating an analysis bottleneck.
  • Ultrafast bootstrap approximation (UFBoot) exists for maximum likelihood but not maximum parsimony.

Purpose of the Study:

  • Introduce MPBoot, an adaptation of UFBoot for maximum parsimony.
  • Enable efficient branch support calculation under maximum parsimony.

Main Methods:

  • MPBoot adapts and extends the UFBoot approach.
  • It computes branch supports using the maximum parsimony principle.
  • MPBoot supports both uniform and non-uniform cost matrices.

Main Results:

  • MPBoot significantly outperforms standard parsimony bootstrap in speed, especially with non-uniform cost matrices.
  • MPBoot achieves better scores more frequently than PAUP* and fast-TNT.
  • MPBoot bootstrap estimates are less conservative and more unbiased on large-scale simulated data.

Conclusions:

  • MPBoot offers an efficient, accurate, and user-friendly alternative for maximum parsimony bootstrap.
  • It demonstrates favorable performance in runtime, tree finding, and bootstrap accuracy.
  • MPBoot is open-source and readily available for use.