A new sequence distance measure for phylogenetic tree construction

被引:236
作者
Otu, HH
Sayood, K
机构
[1] Univ Nebraska, Dept Elect Engn, Lincoln, NE 68503 USA
[2] Harvard Univ, Sch Med, Beth Israel Deaconess Med Ctr Genom Ctr, New England Baptist Bone & Joint Inst, Boston, MA 02215 USA
关键词
D O I
10.1093/bioinformatics/btg295
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
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.
引用
收藏
页码:2122 / 2130
页数:9
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