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Disk-covering, a fast-converging method for phylogenetic tree reconstruction

The evolutionary history of a set of species is represented by a phylogenetic tree, which is a rooted, leaf-labeled tree, where internal nodes represent ancestral species and the leaves represent modern day species. Accurate (or even boundedly inaccurate) topology reconstructions of large and diverg... Full description

Journal Title: Journal of computational biology 1999, Vol.6 (3-4), p.369-386
Main Author: Huson, D H
Other Authors: Nettles, S M , Warnow, T J
Format: Electronic Article Electronic Article
Language: English
Subjects:
Quelle: Alma/SFX Local Collection
Publisher: United States
ID: ISSN: 1066-5277
Link: https://www.ncbi.nlm.nih.gov/pubmed/10582573
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title: Disk-covering, a fast-converging method for phylogenetic tree reconstruction
format: Article
creator:
  • Huson, D H
  • Nettles, S M
  • Warnow, T J
subjects:
  • Algorithms
  • Biometry - methods
  • Evaluation Studies as Topic
  • Markov Chains
  • Models, Statistical
  • Phylogeny
ispartof: Journal of computational biology, 1999, Vol.6 (3-4), p.369-386
description: The evolutionary history of a set of species is represented by a phylogenetic tree, which is a rooted, leaf-labeled tree, where internal nodes represent ancestral species and the leaves represent modern day species. Accurate (or even boundedly inaccurate) topology reconstructions of large and divergent trees from realistic length sequences have long been considered one of the major challenges in systematic biology. In this paper, we present a simple method, the Disk-Covering Method (DCM), which boosts the performance of base phylogenetic methods under various Markov models of evolution. We analyze the performance of DCM-boosted distance methods under the Jukes-Cantor Markov model of biomolecular sequence evolution, and prove that for almost all trees, polylogarithmic length sequences suffice for complete accuracy with high probability, while polynomial length sequences always suffice. We also provide an experimental study based upon simulating sequence evolution on model trees. This study confirms substantial reductions in error rates at realistic sequence lengths.
language: eng
source: Alma/SFX Local Collection
identifier: ISSN: 1066-5277
fulltext: fulltext
issn:
  • 1066-5277
  • 1557-8666
url: Link


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descriptionThe evolutionary history of a set of species is represented by a phylogenetic tree, which is a rooted, leaf-labeled tree, where internal nodes represent ancestral species and the leaves represent modern day species. Accurate (or even boundedly inaccurate) topology reconstructions of large and divergent trees from realistic length sequences have long been considered one of the major challenges in systematic biology. In this paper, we present a simple method, the Disk-Covering Method (DCM), which boosts the performance of base phylogenetic methods under various Markov models of evolution. We analyze the performance of DCM-boosted distance methods under the Jukes-Cantor Markov model of biomolecular sequence evolution, and prove that for almost all trees, polylogarithmic length sequences suffice for complete accuracy with high probability, while polynomial length sequences always suffice. We also provide an experimental study based upon simulating sequence evolution on model trees. This study confirms substantial reductions in error rates at realistic sequence lengths.
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abstractThe evolutionary history of a set of species is represented by a phylogenetic tree, which is a rooted, leaf-labeled tree, where internal nodes represent ancestral species and the leaves represent modern day species. Accurate (or even boundedly inaccurate) topology reconstructions of large and divergent trees from realistic length sequences have long been considered one of the major challenges in systematic biology. In this paper, we present a simple method, the Disk-Covering Method (DCM), which boosts the performance of base phylogenetic methods under various Markov models of evolution. We analyze the performance of DCM-boosted distance methods under the Jukes-Cantor Markov model of biomolecular sequence evolution, and prove that for almost all trees, polylogarithmic length sequences suffice for complete accuracy with high probability, while polynomial length sequences always suffice. We also provide an experimental study based upon simulating sequence evolution on model trees. This study confirms substantial reductions in error rates at realistic sequence lengths.
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