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.2016.12
URN: urn:nbn:de:0030-drops-60884
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Deng, Yun ; Fernández-Baca, David

Fast Compatibility Testing for Rooted Phylogenetic Trees

LIPIcs-CPM-2016-12.pdf (0.6 MB)


We consider the following basic problem in phylogenetic tree construction. Let $\mathcal P = {T_1, ..., T_k} be a collection of rooted phylogenetic trees over various subsets of a set of species. The tree compatibility problem asks whether there is a tree T with the following property: for each i in {1, ..., k}, T_i can be obtained from the restriction of T to the species set of T_i by contracting zero or more edges. If such a tree T exists, we say that P is compatible.

We give a ~O(M_P) algorithm for the tree compatibility problem, where M_P is the total number of nodes and edges in P. Unlike previous algorithms for this problem, the running time of our method does not depend on the degrees of the nodes in the input trees. Thus, it is equally fast on highly resolved and highly unresolved trees.

BibTeX - Entry

  author =	{Yun Deng and David Fern{\'a}ndez-Baca},
  title =	{{Fast Compatibility Testing for Rooted Phylogenetic Trees}},
  booktitle =	{27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)},
  pages =	{12:1--12:12},
  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 =		{},
  URN =		{urn:nbn:de:0030-drops-60884},
  doi =		{10.4230/LIPIcs.CPM.2016.12},
  annote =	{Keywords: Algorithms, computational biology, phylogenetics}

Keywords: Algorithms, computational biology, phylogenetics
Collection: 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)
Issue Date: 2016
Date of publication: 27.06.2016

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