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arXiv 2001.06741q-bio.PEcs.DS
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多物种融合中基因树与物种树一致概率的计算

Computing the probability of gene trees concordant with the species tree in the multispecies coalescent

Jakub Truszkowski, Celine Scornavacca, Fabio Pardi

摘要:

多物种合并的过程模型的系谱关系的基因从几个物种中采样,使有用的预测现象,如不一致的基因树和物种之间的亲缘关系,由于不完整的谱系排序。相反,大量基因树的知识可以告诉我们物种进化的几个方面,例如它的拓扑结构和祖先种群的大小。在这种情况下,一个基本的开放问题是如何有效地计算基因树拓扑结构的概率,给定的物种遗传。虽然已经提出了一些算法来完成这项任务,但它们要么产生近似的结果,要么当它们是精确的时,它们不能扩展到大数据集。在本文中,我们提出了一些进展,准确和有效的计算概率的基因树拓扑结构。我们提供了一个新的算法,给定一个物种树和每个物种的基因采样数,计算的概率,基因树拓扑结构将是一致的物种树。此外,我们提供了一个算法,计算任何特定的基因树拓扑结构与物种树一致的概率。这两种算法都在多项式时间内运行,并已在Python中实现。实验表明,他们能够在几分钟到几小时内分析数千个基因样本的数据集。

英文摘要:

The multispecies coalescent process models the genealogical relationships of genes sampled from several species, enabling useful predictions about phenomena such as the discordance between the gene tree and the species phylogeny due to incomplete lineage sorting. Conversely, knowledge of large collections of gene trees can inform us about several aspects of the species phylogeny, such as its topology and ancestral population sizes. A fundamental open problem in this context is how to efficiently compute the probability of a gene tree topology, given the species phylogeny. Although a number of algorithms for this task have been proposed, they either produce approximate results, or, when they are exact, they do not scale to large data sets. In this paper, we present some progress towards exact and efficient computation of the probability of a gene tree topology. We provide a new algorithm that, given a species tree and the number of genes sampled for each species, calculates the probability that the gene tree topology will be concordant with the species tree. Moreover, we provide an algorithm that computes the probability of any specific gene tree topology concordant with the species tree. Both algorithms run in polynomial time and have been implemented in Python. Experiments show that they are able to analyse data sets where thousands of genes are sampled, in a matter of minutes to hours.

机构、总结、中文摘要均由AI分析而来,可能存在错误,请以论文正文为准。

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