IEEE/ACM Trans Comput Biol Bioinform. 2021 Nov-Dec;18(6):2855-2861. doi: 10.1109/TCBB.2021.3101278. Epub 2021 Dec 8.
We present the phylogenetic quartet reconstruction method SAQ (Semi-Algebraic Quartet reconstruction). SAQ is consistent with the most general Markov model of nucleotide substitution and, in particular, it allows for rate heterogeneity across lineages. Based on the algebraic and semi-algebraic description of distributions that arise from the general Markov model on a quartet, the method outputs normalized weights for the three trivalent quartets (which can be used as input of quartet-based methods). We show that SAQ is a highly competitive method that outperforms most of the well known reconstruction methods on data simulated under the general Markov model on 4-taxon trees. Moreover, it also achieves a high performance on data that violates the underlying assumptions.
我们提出了系统发育四分体重建方法 SAQ（半代数四分体重建）。SAQ 与核苷酸替代的最通用的 Markov 模型一致，特别是它允许谱系之间的速率异质性。基于一般 Markov 模型在四分体上产生的分布的代数和半代数描述，该方法输出三个三分体的归一化权重（可作为基于四分体的方法的输入）。我们表明，SAQ 是一种极具竞争力的方法，在四分类树的一般 Markov 模型下模拟数据时，它优于大多数知名的重建方法。此外，它在违反基本假设的数据上也表现出很高的性能。
