title: Parametric analysis of alignment and phylogenetic uncertainty.
abstract: 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.
authors.affiliation: Department of Integrative Biology, University of California at Berkeley, CA 94720-3140, USA.
authors.forename: Anna-Sapfo
authors.initials: AS
authors.lastname: Malaspinas
authors.forename: Nicholas
authors.initials: N
authors.lastname: Eriksson
authors.forename: Peter
authors.initials: P
authors.lastname: Huggins
mesh_terms: D000426:Alcohol Dehydrogenase / Q000235:genetics; D000465:Algorithms; D000818:Animals; D001483:Base Sequence / Q000235:genetics; D004330:Drosophila / Q000235:genetics; D029721:Drosophila Proteins / Q000235:genetics; D007438:Introns / Q000235:genetics; D016011:Normal Distribution; D010802:Phylogeny; D011336:Probability; D016415:Sequence Alignment / Q000379:methods / Q000706:statistics & numerical data*; D012689:Sequence Homology, Nucleic Acid; D012984:Software; D050857:Synaptotagmins / Q000235:genetics
chemical_list: D029721:Drosophila Proteins; D050857:Synaptotagmins; C073796:ADH protein, Drosophila; D000426:Alcohol Dehydrogenase