License: Creative Commons Attribution 3.0 Unported license (CC-BY 3.0)
When quoting this document, please refer to the following
DOI: 10.4230/LIPIcs.WABI.2017.9
URN: urn:nbn:de:0030-drops-76529
URL: https://drops.dagstuhl.de/opus/volltexte/2017/7652/
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Crochemore, Maxime ; Francisco, Alexandre P. ; Pissis, Solon P. ; Vaz, Cátia

Towards Distance-Based Phylogenetic Inference in Average-Case Linear-Time

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Abstract

Computing genetic evolution distances among a set of taxa dominates the running time of many phylogenetic inference methods. Most of genetic evolution distance definitions rely, even if indirectly, on computing the pairwise Hamming distance among sequences or profiles. We propose here an average-case linear-time algorithm to compute pairwise Hamming distances among a set of taxa under a given Hamming distance threshold. This article includes both a theoretical analysis and extensive experimental results concerning the proposed algorithm. We further show how this algorithm can be successfully integrated into a well known phylogenetic inference method.

BibTeX - Entry

@InProceedings{crochemore_et_al:LIPIcs:2017:7652,
  author =	{Maxime Crochemore and Alexandre P. Francisco and Solon P. Pissis and C{\'a}tia Vaz},
  title =	{{Towards Distance-Based Phylogenetic Inference in Average-Case Linear-Time}},
  booktitle =	{17th International Workshop on Algorithms in Bioinformatics (WABI 2017)},
  pages =	{9:1--9:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-050-7},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{88},
  editor =	{Russell Schwartz and Knut Reinert},
  publisher =	{Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{http://drops.dagstuhl.de/opus/volltexte/2017/7652},
  URN =		{urn:nbn:de:0030-drops-76529},
  doi =		{10.4230/LIPIcs.WABI.2017.9},
  annote =	{Keywords: computational biology, phylogenetic inference, Hamming distance}
}

Keywords: computational biology, phylogenetic inference, Hamming distance
Collection: 17th International Workshop on Algorithms in Bioinformatics (WABI 2017)
Issue Date: 2017
Date of publication: 11.08.2017


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