DNA assembly with gaps (Dawg): simulating sequence evolution
DNA assembly with gaps (Dawg): simulating sequence evolution
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DOI：
10.1093/bioinformatics/bti1200
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发表时间：
2005-01-01
期刊：
影响因子：
5.8
通讯作者：
Cartwright, RA
中科院分区：
文献类型：
--
作者：
Cartwright, RA
动机：分类群之间的关系是使用系统发育方法和程序从生物学数据中推断出来的。很少有已知的遗传学可以用来检验我们推论的准确性。因此，在缺乏生物学数据的情况下，必须使用模拟数据来测试产生这些推断的方法的准确性。研究人员有有限的或不存在的选项，用于模拟有用的研究插入，缺失和比对系统发育的准确性的影响。结果：为了满足这一差距，我已经开发了一种新的算法的插入缺失形成，并将其纳入一个新的，灵活的，便携式的应用程序序列模拟。该应用程序称为Dawg，使用具有伽马和不变速率异质性的鲁棒通用时间可逆模型和一种新的长度依赖的indel形成模型来模拟DNA序列在连续时间内的系统发育进化。完成后，Dawg产生模拟序列的真实比对。与其他应用程序不同，Dawg允许插入缺失长度通过生物现实的幂律显式分布。有许多选项可供用户自定义其模拟和结果。因为如果不能估计生物学上真实的参数，用插入缺失进行模拟将是有问题的，所以Dawg提供了一个脚本，该脚本可以从序列数据估计插入缺失形成的参数。Dawg应用于四个叶绿体trnK内含子的序列。它被用来参数化地自举（bootstrap）估计遗传学的插入缺失形成速率。因为Dawg可以帮助序列数据的参数化自举，所以它在遗传学之外是有用的，例如研究比对算法或分子进化的参数。
Motivation: Relationships amongst taxa are inferred from biological data using phylogenetic methods and procedures. Very few known phylogenies exist against which to test the accuracy of our inferences. Therefore, in the absence of biological data, simulated data must be used to test the accuracy of methods which produce these inferences. Researchers have limited or non-existent options for simulations useful for studying the impact of insertions, deletions, and alignments on phylogenetic accuracy.Results: To satisfy this gap I have developed a new algorithm of indel formation and incorporated it into a new, flexible, and portable application for sequence simulation. The application, called Dawg, simulates phylogenetic evolution of DNA sequences in continuous time using the robust general time reversible model with gamma and invariant rate heterogeneity and a novel length-dependent model of indel formation. On completion, Dawg produces the true alignment of the simulated sequences. Unlike other applications, Dawg allows indel lengths to be explicitly distributed via a biologically realistic power law. Many options are available to allow users to customize their simulations and results. Because simulating with indels would be problematic if biologically realistic parameters could not be estimated, a script is provided with Dawg that can estimate the parameters of indel formation from sequence data. Dawg was applied to the sequences of four chloroplast trnK introns. It was used to parametrically bootstrap an estimation of the rate of indel formation for the phylogeny. Because Dawg can assist in parametric bootstrapping of sequence data it is useful beyond phylogenetics, such as studying alignment algorithms or parameters of molecular evolution.