Simulating DNA coding sequence evolution with EvolveAGene 3
Simulating DNA coding sequence evolution with EvolveAGene 3
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DOI：
10.1093/molbev/msn008
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发表时间：
2008-04-01
影响因子：
10.7
通讯作者：
Hall, Barry G.
中科院分区：
文献类型：
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作者：
Hall, Barry G.
基于分子序列多重比对的系统发育重建对现代生物学的大多数分支都很重要，也是分子进化的核心。理解大分子之间的历史关系依赖于实现各种分析方法的计算机程序。因为不可能确切地知道这些历史关系，所以评估方法的准确性和实现它们的程序需要使用实际模拟DNA序列进化的程序。EvolveAGene 3是一个现实的编码序列模拟程序，它将突变与选择分离开来，并允许用户设置选择条件，包括序列内选择强度的可变区域和分支上选择强度的变化。变异包括碱基替换、插入和缺失。据我所知，这是唯一一个可以模拟完整编码序列进化的程序。输出结果包括真树和所得到的编码序列和相应蛋白质序列的真比对。日志文件报告了每种碱基替换的频率，转换与翻转替换的比率，indel与碱基替换突变的比率，以及沉默和氨基酸替换突变的数量。通过比较模拟数据集的d(N)/d(S)比率、过渡与转换替换的比率、indel与碱基替换突变的比率，以及来自“金标准”BaliBase结构比对集合的真实数据集的参数，评估了数据集的真实性。结果表明，EvolveAGene 3生成的数据集与真实数据集非常相似，因此EvolveAGene 3是一个真实的模拟程序，可用于评估分子进化中的各种程序和方法。
Phylogenetic reconstruction based upon multiple alignments of molecular sequences is important to most branches of modern biology and is central to molecular evolution. Understanding the historical relationships among macromolecules depends upon computer programs that implement a variety of analytical methods. Because it is impossible to know those historical relationships with certainty, assessment of the accuracy of methods and the programs that implement them requires the use of programs that realistically simulate the evolution of DNA sequences. EvolveAGene 3 is a realistic coding sequence simulation program that separates mutation from selection and allows the user to set selection conditions, including variable regions of selection intensity within the sequence and variation in intensity of selection over branches. Variation includes base substitutions, insertions, and deletions. To the best of my knowledge, it is the only program available that simulates the evolution of intact coding sequences. Output includes the true tree and true alignments of the resulting coding sequence and corresponding protein sequences. A log file reports the frequencies of each kind of base substitution, the ratio of transition to transversion substitutions, the ratio of indel to base substitution mutations, and the numbers of silent and amino acid replacement mutations. The realism of the data sets has been assessed by comparing the d(N)/d(S) ratio, the ratio of transition to transversion substitutions, and the ratio of indel to base substitution mutations of the simulated data sets with those parameters of real data sets from the "gold standard" BaliBase collection of structural alignments. Results show that the data sets produced by EvolveAGene 3 are very similar to real data sets, and EvolveAGene 3 is therefore a realistic simulation program that can be used to evaluate a variety of programs and methods in molecular evolution.