| Parametric Maximum Parsimonious Reconstruction on Trees. | |
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MedLine Citation:
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PMID: 20737226 Owner: NLM Status: In-Data-Review |
Abstract/OtherAbstract:
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We give a formal study of the relationships between the transition cost parameters and the generalized maximum parsimonious reconstructions of unknown (ancestral) binary character states [Formula: see text] over a phylogenetic tree. As a main result, we show there are two thresholds [Formula: see text] and [Formula: see text], generally confounded, associated to each node n of the phylogenetic tree and such that there exists a maximum parsimonious reconstruction associating state [Formula: see text] to n (resp. state [Formula: see text] to n) if the ratio "[Formula: see text]-cost"/"[Formula: see text]-cost" is smaller than [Formula: see text] (resp. greater than [Formula: see text]). We propose a dynamic programming algorithm computing these thresholds in a quadratic time with the size of tree.We briefly illustrate some possible applications of this work over a biological dataset. In particular, the thresholds provide a natural way to quantify the degree of support for states reconstructed as well as to determine what kind of evolutionary assumptions in terms of costs are necessary to a given reconstruction. |
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Authors:
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Gilles Didier |
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Publication Detail:
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Type: Journal Article Date: 2010-08-25 |
Journal Detail:
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Title: Bulletin of mathematical biology Volume: 73 ISSN: 1522-9602 ISO Abbreviation: Bull. Math. Biol. Publication Date: 2011 Jul |
Date Detail:
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Created Date: 2011-05-18 Completed Date: - Revised Date: - |
Medline Journal Info:
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Nlm Unique ID: 0401404 Medline TA: Bull Math Biol Country: United States |
Other Details:
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Languages: eng Pagination: 1477-502 Citation Subset: IM |
Affiliation:
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Institut de Mathématiques de Luminy CNRS-UMR 6206, Campus de Luminy, Case 907, 13288, Marseille Cedex 9, France, didier@iml.univ-mrs.fr. |
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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