基于spr的树调和:非二叉树和多解

Cuong V. Than, L. Nakhleh
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引用次数: 16

摘要

SPR(子树修剪和再嫁接)操作被用作协调不一致的系统发育树的基础,特别是用于检测和分析非树状进化历史,如水平基因转移、杂交物种形成和重组。基于spr的树调和问题已被证明是np困难的,并且设计了几种有效的启发式方法来解决它。这些启发式的一个主要缺点是,在大多数情况下,它们不能适当地处理非二叉树。此外,当计算多个最优调和时,它们的计算效率会受到显著影响。在本文中,我们提出了一种算法技术,可以有效地对不一定是二值的树进行基于spr的和解。此外,我们提出了分而治之的方法,使多个最优调和的有效计算。我们已经在PhyloNet软件包中实现了我们的技术,该软件包可在http://bioinfo.cs.rice.edu上公开获得。由此产生的方法在速度方面优于所有现有方法,并且在准确性方面至少与这些方法一样好。
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SPR-based Tree Reconciliation: Non-binary Trees and Multiple Solutions
The SPR (subtree prune and regraft) operation is used as the basis for reconciling incongruent phylogenetic trees, particularly for detecting and analyzing non-treelike evolutionary histories such as horizontal gene transfer, hybrid speciation, and recombination. The SPR-based tree reconciliation problem has been shown to be NP-hard, and several efficient heuristics have been designed to solve it. A major drawback of these heuristics is that for the most part they do not handle non-binary trees appropriately. Further, their computational efficiency suffers significantly when computing multiple optimal reconciliations. In this paper, we present algorithmic techniques for efficient SPR-based reconciliation of trees that are not necessarily binary. Further, we present divide-and-conquer approaches that enable efficient computing of multiple optimal reconciliations. We have implemented our techniques in the PhyloNet software package, which is publicly available at http://bioinfo.cs.rice.edu. The resulting method outperforms all existing methods in terms of speed, and performs at least as well as those methods in terms of accuracy.
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