A new sequence distance measure for phylogenetic tree construction
A new sequence distance measure for phylogenetic tree construction
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DOI：
10.1093/bioinformatics/btg295
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发表时间：
2003-11-01
期刊：
影响因子：
5.8
通讯作者：
Sayood, K
中科院分区：
文献类型：
--
作者：
Otu, HH;Sayood, K
动机：大多数现有的系统发育推断方法使用多个序列比对，并假设某种类型的进化模型。多重比对策略并不适用于所有类型的数据，例如全基因组系统发育，进化模型可能并不总是正确的。利用Lempel-Ziv复杂度，提出了一种基于序列间相对信息的序列距离度量方法。所得到的距离矩阵可用于构建系统发育树。结果：该方法不需要序列比对，且完全自动化。该算法已经成功地为真实数据集和模拟数据集构建了一致的系统发生图。
Motivation: Most existing approaches for phylogenetic inference use multiple alignment of sequences and assume some sort of an evolutionary model. The multiple alignment strategy does not work for all types of data, e.g. whole genome phylogeny, and the evolutionary models may not always be correct. We propose a new sequence distance measure based on the relative information between the sequences using Lempel-Ziv complexity. The distance matrix thus obtained can be used to construct phylogenetic trees.Results: The proposed approach does not require sequence alignment and is totally automatic. The algorithm has successfully constructed consistent phylogenies for real and simulated data sets.