基于合并器的四重频率局部分支支持度的快速计算
Fast coalescent-based computation of local branch support from quartet frequencies
摘要：
物种树重建是复杂的不完全谱系排序（ILS）的影响，通常由多物种合并模型建模。虽然已经有了很大的进展，在开发方法，估计一个物种树的基因树的集合，很少注意到已经支付了快速和准确的方法量化支持。在本文中，我们提出了一个快速算法来计算基于四分支持度的每个分支的一个给定的物种树关于一组给定的基因树。然后，我们展示了如何在多物种合并模型的上下文中使用四重支持来计算i）分支在物种树中的局部后验概率和ii）合并单元中分支的长度。我们评估了一组广泛的模拟和生物学数据的局部后验概率的精度和召回率，并表明它具有非常高的精度和提高召回相比，多位点自举。当基因树误差较小时，估计的分支长度是高度准确的，但当基因树估计误差增加时，估计的分支长度被低估。分支长度和局部后验概率的计算作为ASTRAL的一个新功能被实现。
英文摘要：
Species tree reconstruction is complicated by effects of Incomplete Lineage Sorting (ILS), commonly modeled by the multi-species coalescent model. While there has been substantial progress in developing methods that estimate a species tree given a collection of gene trees, less attention has been paid to fast and accurate methods of quantifying support. In this paper, we propose a fast algorithm to compute quartet-based support for each branch of a given species tree with regard to a given set of gene trees. We then show how the quartet support can be used in the context of the multi-species coalescent model to compute i) the local posterior probability that the branch is in the species tree and ii) the length of the branch in coalescent units. We evaluate the precision and recall of the local posterior probability on a wide set of simulated and biological data, and show that it has very high precision and improved recall compared to multi-locus bootstrapping. The estimated branch lengths are highly accurate when gene trees have little error, but are underestimated when gene tree estimation error increases. Computation of both branch length and local posterior probability is implemented as a new feature in ASTRAL.
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。
