Data from: A consensus method for ancestral recombination graphs

We propose a consensus method for ancestral recombination graphs (ARGs) that generates a single ARG representing commonalities among a cloud of ARGs defined for the same genomic region and set of taxa. Our method, which we call “threshold consensus,” treats a genomic location as a potential recombination breakpoint only if the number of ARGs in the cloud possessing a breakpoint at that location exceeds a chosen threshold. The estimate is further refined by ignoring recombinations that do not change the local tree topologies, as well as collapsing breakpoint locations separated only by invariant sites. We test the threshold consensus algorithm, using a range of threshold values, on simulated ARGs inferred by a genealogy sampling algorithm, and evaluate accuracy of breakpoints and local topologies in the resulting consensus ARGs.我们提出了一种针对祖先重组图（ancestral recombination graphs, ARGs）的共识构建方法，该方法可生成单一的祖先重组图，用以表征针对同一基因组区域与类群集合所构建的ARGs集合中的共性特征。我们将该方法命名为“阈值共识法”，其判定规则为：仅当集合中在某一基因组位点存在重组断点的ARGs数量超过预设阈值时，才将该位点视为潜在重组断点。为进一步优化估计结果，本方法会忽略那些不会改变局部树拓扑结构的重组事件，同时合并仅被不变位点分隔的断点位点。我们采用谱系采样算法所推断的模拟ARGs数据集，针对一系列阈值参数对阈值共识算法开展了测试，并对最终所得共识ARGs的断点位置与局部树拓扑结构的准确性进行了评估。