SAQ：半代数四重重建方法
SAQ: semi-algebraic quartet reconstruction method
摘要：
提出了系统发育四重态重建方法SAQ（Semi-algebraic quartet reconstruction）。SAQ与核苷酸取代的最一般的马尔可夫模型一致，特别是，它允许跨谱系的速率异质性。基于四元组上的一般马尔可夫模型产生的分布的代数和半代数描述，该方法输出三个三价四元组的归一化权重（其可用作四元组基方法的输入）。我们表明，SAQ是一个非常有竞争力的方法，优于大多数众所周知的重建方法的数据模拟下的一般马尔可夫模型的4分类树。此外，它还在违反基本假设的数据上实现了高性能。
英文摘要：
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.
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