Incorporating information from length-mutational events into phylogenetic analysis
Incorporating information from length-mutational events into phylogenetic analysis
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DOI：
10.1016/j.ympev.2005.07.011
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发表时间：
2006-03-01
影响因子：
4.1
通讯作者：
Müller, K
中科院分区：
文献类型：
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作者：
Müller, K
随着使用长度可变 DNA 序列的系统发育研究的数量不断增加，将长度突变事件的信息纳入系统发育分析变得越来越重要。描述了一种新方法，即改良的复杂插入缺失编码，其目的是最大化从明确比对的序列区域或可以安全地建立间隙彼此的主要相对位置的区域中保留的系统发育信息。描述了一种算法，允许将该方法应用于所有理论上可能的间隙核苷酸模式。引入了一种独立于平台的计算机程序，该程序可以自动执行新方法以及之前发布的几种编码方案。讨论了与先前发表的插入缺失编码方法的差异以及将不明确对齐的区域整合到系统发育分析中的差异。 (c) 2005 Elsevier Inc. 保留所有权利。
With the growing number of phylogenetic studies that use length variable DNA sequences, incorporating information from length-mutational events into phylogenetic analysis is becoming increasingly important. A new method, modified complex indel coding is described that aims at maximizing the phylogenetic information retained from unambiguously aligned sequence regions or regions where the principal relative position of gaps to one another can be safely established. An algorithm is described that allows application of the method to all theoretically possible gap-nucleotide patterns. A platform-independent computer program is introduced that automates the new method as well as several previously published coding schemes. Differences to previously published indel coding approaches as well as to the integration of ambiguously aligned regions into phylogenetic analysis are discussed. (c) 2005 Elsevier Inc. All rights reserved.