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- Title
Parametric analysis of alignment and phylogenetic uncertainty.
- Authors
Malaspinas, Anna-Sapfo; Eriksson, Nicholas; Huggins, Peter
- 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.
- Publication
Bulletin of mathematical biology, 2011, Vol 73, Issue 4, p795
- ISSN
1522-9602
- Publication type
Journal Article
- DOI
10.1007/s11538-010-9610-8