Isolating - a new resampling method for gene order data

Jian Shi, W. Arndt, Fei Hu, Jijun Tang
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引用次数: 4

Abstract

The purpose of using resampling methods on phylogenetic data is to estimate the confidence value of branches. In recent years, bootstrapping and jackknifing are the two most popular resampling schemes which are widely used in biological reserach. However, for gene order data, traditional bootstrap procedures can not be applied because gene order data is viewed as one character with various states. Experience in the biological community has shown that jackknifing is a useful means of determining the confidence value of a gene order phylogeny. When genomes are distant, however, applying jackknifing tends to give low confidence values to many valid branches, causing them to be mistakenly removed. In this paper, we propose a new method that overcomes this disadvantage of jackknifing and achieves better accuracy and confidence values for gene order data. Compared to jackknifing, our experimental results show that the proposed method can produce phylogenies with lower error rates and much stronger support for good branches. We also establish a theoretic lower bound regarding how many genes should be isolated, which is confirmed empirically.
分离——一种新的基因序列重采样方法
对系统发育数据使用重采样方法的目的是估计分支的置信值。近年来,在生物研究中应用最广泛的两种重采样方案是自举和夹持。然而,对于基因序列数据,由于基因序列数据被视为具有多种状态的一个字符,传统的自举方法无法应用。生物界的经验表明,jackknife是确定基因序系统发育置信度的有效方法。然而,当基因组距离较远时,应用jackknife往往会给许多有效分支提供低置信度值,从而导致它们被错误地移除。在本文中,我们提出了一种新的方法,克服了这一缺点,并获得了更好的准确性和置信度的基因序列数据。与jackkifing相比,我们的实验结果表明,该方法可以产生更低的错误率和更强的支持好的分支的系统发育。我们还建立了一个关于应该分离多少基因的理论下限,这是经验证实的。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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