论文标题

评估系统发育方法的亚弹药方法的相对性能

Evaluation of the relative performance of the subflattenings method for phylogenetic inference

论文作者

Stevenson, Joshua, Holland, Barbara, Charleston, Michael, Sumner, Jeremy

论文摘要

使用序列比对中的模式计数,扁平和亚弹片的代数特性提供了直接的方法,可用于识别真正的系统发育中的边缘 - 并扩展完整的树。一组分类单元之间可能的内部边缘数量相对较少(与二进制树的数量相比)使这些方法具有吸引力,但是可以做更多的方法来评估它们用于推断系统发育树的有效性。尤其是子弹药,我们的工作在这方面取得了进步。我们介绍了用于构造和评估拆分子弹的软件,并利用多种方法使计算子弹片更加易于处理。然后,我们介绍了我们进行的模拟结果,以将亚面的有效性与扁平分数分布和对可能偏见的敏感性相比。我们发现,在我们检查的树上的分裂分数的分布方面,亚弹片的性能与扁平化相似,但可能会受到偏分尺寸/平衡和长分支吸引力所产生的偏差的影响。这些见解对于开发有效的算法来利用这些工具来推断系统发育树很有用。

The algebraic properties of flattenings and subflattenings provide direct methods for identifying edges in the true phylogeny -- and by extension the complete tree -- using pattern counts from a sequence alignment. The relatively small number of possible internal edges among a set of taxa (compared to the number of binary trees) makes these methods attractive, however more could be done to evaluate their effectiveness for inferring phylogenetic trees. This is the case particularly for subflattenings, and our work makes progress in this area. We introduce software for constructing and evaluating subflattenings for splits, utilising a number of methods to make computing subflattenings more tractable. We then present the results of simulations we have performed in order to compare the effectiveness of subflattenings to that of flattenings in terms of split score distributions, and susceptibility to possible biases. We find that subflattenings perform similarly to flattenings in terms of the distribution of split scores on the trees we examined, but may be less affected by bias arising from both split size/balance and long branch attraction. These insights are useful for developing effective algorithms to utilise these tools for the purpose of inferring phylogenetic trees.

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