Parametric Analysis of Alignment and Phylogenetic Uncertainty

  • Anna-Sapfo Malaspinas
  • Nicholas Eriksson
  • Peter Huggins
Original Article


To infer a phylogenetic tree from a set of DNA sequences, typically a multiple alignment is first used to obtain homologous bases. The inferred phylogeny can be very sensitive to how the alignment was created. We develop tools for analyzing the robustness of phylogeny to perturbations in alignment parameters in the NW algorithm. Our main tool is parametric alignment, with novel improvements that are of general interest in parametric inference. Using parametric alignment and a Gaussian distribution on alignment parameters, we derive probabilities of optimal alignment summaries and inferred phylogenies. We apply our method to analyze intronic sequences from Drosophila flies. We show that phylogeny estimates can be sensitive to the choice of alignment parameters, and that parametric alignment elucidates the relationship between alignment parameters and reconstructed trees.


Phylogenetics Parametric alignment Multiple alignment Polytopes 

Copyright information

© Society for Mathematical Biology 2011

Authors and Affiliations

  • Anna-Sapfo Malaspinas
    • 1
  • Nicholas Eriksson
    • 2
  • Peter Huggins
    • 3
  1. 1.Department of Integrative BiologyUniversity of California at BerkeleyBerkeleyUSA
  2. 2.23andmeMountain ViewUSA
  3. 3.Lane Center for Computational BiologyCarnegie Mellon UniversityPittsburghUSA

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