LIPIcs.CPM.2016.12.pdf
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Fast Compatibility Testing for Rooted Phylogenetic Trees
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27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016)
Series: Leibniz International Proceedings in Informatics (LIPIcs)
Conference: Annual Symposium on Combinatorial Pattern Matching (CPM) - License:
Creative Commons Attribution 3.0 Unported license
- Publication Date: 2016-06-27
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Yun Deng and David Fernández-Baca. Fast Compatibility Testing for Rooted Phylogenetic Trees. In 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 54, pp. 12:1-12:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)
https://doi.org/10.4230/LIPIcs.CPM.2016.12
Abstract
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.
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- Algorithms
- computational biology
- phylogenetics
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