文章基本信息

标题：Efficient Non-Binary Gene Tree Resolution with Weighted Reconciliation Cost
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作者：Manuel Lafond ; Emmanuel Noutahi ; Nadia El-Mabrouk 等
期刊名称：LIPIcs : Leibniz International Proceedings in Informatics
电子版ISSN：1868-8969
出版年度：2016
卷号：54
页码：14:1-14:12
DOI：10.4230/LIPIcs.CPM.2016.14
出版社：Schloss Dagstuhl -- Leibniz-Zentrum fuer Informatik
摘要：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.
关键词：gene tree; polytomy; reconciliation; resolution; weighted cost; phylogeny