SODA: multi-locus species delimitation using quartet frequencies
SODA: multi-locus species delimitation using quartet frequencies
复制标题
SODA：使用四重频率进行多位点物种界定
DOI：
10.1093/bioinformatics/btaa1010
复制
发表时间：
2020
期刊：
影响因子：
5.8
通讯作者：
Mirarab, Siavash
中科院分区：
文献类型：
--
作者：
Rabiee, Maryam;Mirarab, Siavash
动机物种界定，即决定如何将一组生物体分组为称为物种的单位的过程，是计算进化生物学中最具挑战性的问题之一。虽然存在许多用于物种界定的方法，但大多数方法都基于合并理论，但很少有方法可以扩展到非常大的数据集，并且扩展的方法往往不准确。物种定界与从不一致基因树推断物种树密切相关，这是近年来迅速发展的一个问题。结果在本文中，我们基于最近基于四重奏的物种树估计方法的准确性和可扩展性，提出了一种称为 SODA 的新物种定界方法。 SODA 在很大程度上依赖于最近开发的一种方法来测试物种树中的零分支长度。在广泛的模拟中，我们表明 SODA 可以轻松扩展到非常大的数据集，同时保持高精度。可用性和实现此处提供的代码和数据可在 https://github.com/maryamrabiee/SODA 上获取。补充信息补充数据可在 Bioinformaticsonline 上获取。
MotivationSpecies delimitation, the process of deciding how to group a set of organisms into units called species, is one of the most challenging problems in computational evolutionary biology. While many methods exist for species delimitation, most based on the coalescent theory, few are scalable to very large datasets, and methods that scale tend to be not accurate. Species delimitation is closely related to species tree inference from discordant gene trees, a problem that has enjoyed rapid advances in recent years.ResultsIn this article, we build on the accuracy and scalability of recent quartet-based methods for species tree estimation and propose a new method called SODA for species delimitation. SODA relies heavily on a recently developed method for testing zero branch length in species trees. In extensive simulations, we show that SODA can easily scale to very large datasets while maintaining high accuracy.Availability and implementationThe code and data presented here are available on https://github.com/maryamrabiee/SODA.Supplementary informationSupplementary data are available atBioinformaticsonline.