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.CPM.2016.14
URN: urn:nbn:de:0030-drops-60907
URL: http://dagstuhl.sunsite.rwth-aachen.de/volltexte/2016/6090/
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Lafond, Manuel ; Noutahi, Emmanuel ; El-Mabrouk, Nadia

Efficient Non-Binary Gene Tree Resolution with Weighted Reconciliation Cost

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Abstract

Polytomies in gene trees are multifurcated nodes corresponding to unresolved parts of the tree, usually due to insufficient differentiation between sequences of homologous gene copies. Apart from gene sequences, other information such as that contained in the species tree can be used to resolve such intricate parts of a gene tree. The problem of resolving a multifurcated tree has been considered by many authors, the objective function often being the number of duplications and losses reflected by the reconciliation of the resolved gene tree with the species tree. Here, we present PolytomySolver, an algorithm accounting for a more general model allowing different costs for duplications and losses per species. The time complexity of this algorithm is linear for the unit cost and is quadratic for the general cost, which outperforms the best known solutions so far by a linear factor. We show on simulated trees that the gain in theoretical complexity has a real practical impact on running times.

BibTeX - Entry

@InProceedings{lafond_et_al:LIPIcs:2016:6090,
  author =	{Manuel Lafond and Emmanuel Noutahi and Nadia El-Mabrouk},
  title =	{{Efficient Non-Binary Gene Tree Resolution with Weighted Reconciliation Cost}},
  booktitle =	{27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)},
  pages =	{14:1--14:12},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-012-5},
  ISSN =	{1868-8969},
  year =	{2016},
  volume =	{54},
  editor =	{Roberto Grossi and Moshe Lewenstein},
  publisher =	{Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{http://drops.dagstuhl.de/opus/volltexte/2016/6090},
  URN =		{urn:nbn:de:0030-drops-60907},
  doi =		{10.4230/LIPIcs.CPM.2016.14},
  annote =	{Keywords: gene tree, polytomy, reconciliation, resolution, weighted cost, phylogeny}
}

Keywords: gene tree, polytomy, reconciliation, resolution, weighted cost, phylogeny
Collection: 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)
Issue Date: 2016
Date of publication: 27.06.2016

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