论文标题
SAQ：半代数四重奏重建方法
SAQ: semi-algebraic quartet reconstruction method
论文作者
论文摘要
我们介绍系统发育四重奏重建方法SAQ（半代数四重奏重建）。 SAQ与最通用的Markov核苷酸取代模型一致，尤其是它允许跨谱系的速率异质性。基于由四重奏上的一般马尔可夫模型产生的分布的代数和半代数描述，该方法为三个三价四重奏的归一化权重（可以用作四重奏基本方法的输入）。我们表明，SAQ是一种高度竞争的方法，它在4-Taxon树上的一般马尔可夫模型下模拟的数据上胜过大多数众所周知的重建方法。此外，它还可以在违反基本假设的数据上实现高性能。
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-base 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.
