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首页> 外文期刊>Computational Biology and Bioinformatics, IEEE/ACM Transactions on >Comparison of Tree-Child Phylogenetic Networks
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Comparison of Tree-Child Phylogenetic Networks

机译：树儿童系统进化网络的比较

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摘要

Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of nontreelike evolutionary events, like recombination, hybridization, or lateral gene transfer. While much progress has been made to find practical algorithms for reconstructing a phylogenetic network from a set of sequences, all attempts to endorse a class of phylogenetic networks (strictly extending the class of phylogenetic trees) with a well-founded distance measure have, to the best of our knowledge and with the only exception of the bipartition distance on regular networks, failed so far. In this paper, we present and study a new meaningful class of phylogenetic networks, called tree-child phylogenetic networks, and we provide an injective representation of these networks as multisets of vectors of natural numbers, their path multiplicity vectors. We then use this representation to define a distance on this class that extends the well-known Robinson-Foulds distance for phylogenetic trees and to give an alignment method for pairs of networks in this class. Simple polynomial algorithms for reconstructing a tree-child phylogenetic network from its path multiplicity vectors, for computing the distance between two tree-child phylogenetic networks and for aligning a pair of tree-child phylogenetic networks, are provided. They have been implemented as a Perl package and a Java applet, which can be found at http://bioinfo.uib.es/~recerca/phylonetworks/mudistance/.
机译：系统发育网络是系统树的概括，可以表示非树状进化事件，例如重组，杂交或侧向基因转移。尽管找到了从一组序列重建系统进化网络的实用算法方面已经取得了很大进展，但所有尝试以可靠的距离度量来支持一类系统进化网络（严格扩展系统进化树的类别）的尝试都已经到了据我们所知，除常规网络上的两分距离外，到目前为止都失败了。在本文中，我们提出并研究了一种新的有意义的系统发育网络类，称为树子系统发育网络，并以自然数向量，路径多重性向量的多集形式提供了这些网络的内射表示。然后，我们使用此表示法在此类上定义一个距离，该距离扩展了系统树的众所周知的Robinson-Foulds距离，并为此类中的网络对提供了对齐方法。提供了简单的多项式算法，该算法可从其路径多重性向量重建树形树种系统网络，计算两个树形树种系统网络之间的距离，并对齐一对树形树种系统网络。它们已作为Perl软件包和Java小程序实现，可以在http://bioinfo.uib.es/~recerca/phylonetworks/mudistance/中找到。

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