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Multiple sequence alignment accuracy and phylogenetic inference.

T Heath Ogden1, Michael S Rosenberg

  • 1Center for Evolutionary Functional Genomics, The Biodesign Institute, and the School of Life Sciences, Arizona State University, Tempe, Arizona 85287-4501, USA. heath_ogden@asu.edu

Systematic Biology
|April 14, 2006
PubMed
Summary
This summary is machine-generated.

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Accurate sequence alignment is crucial for reliable phylogenetic inference. Higher alignment error generally leads to decreased topological accuracy, especially in pectinate tree shapes, impacting evolutionary studies.

Area of Science:

  • Computational Biology
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Phylogenetic reconstruction accuracy is often debated regarding its dependence on sequence alignment versus reconstruction methods.
  • Understanding the impact of alignment accuracy is vital for robust evolutionary analyses.

Purpose of the Study:

  • To investigate the role of sequence alignment accuracy in phylogenetic inference.
  • To quantify the effect of alignment errors on the accuracy of reconstructed phylogenies.

Main Methods:

  • Simulated sequence data with insertions and deletions across various tree shapes (pectinate, balanced, random) and evolutionary models.
  • Assessed alignment accuracy using measures for the total dataset and individual branches.
  • Compared phylogenetic reconstruction accuracy using Maximum Likelihood, Bayesian, Neighbor Joining, and Maximum Parsimony methods.

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Main Results:

  • Increased alignment error correlated with decreased topological accuracy, particularly for pectinate tree shapes.
  • Balanced, ultrametric, equal branch length tree shapes showed minimal impact from alignment inaccuracy on average.
  • Branch length and neighboring branch lengths influenced alignment accuracy, with longer neighboring branches being a major factor in topological accuracy.

Conclusions:

  • Multiple-sequence alignment accuracy significantly impacts downstream phylogenetic reconstruction.
  • Reconstruction methods like Maximum Likelihood and Bayesian generally yield more accurate trees than Neighbor Joining and Maximum Parsimony.
  • Alignment accuracy is a critical consideration for reliable phylogenetic inference, especially for certain evolutionary histories.