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.本研究提出一种针对祖先重组图（ancestral recombination graphs, ARGs）的共识构建方法，可生成单个ARG，用以表征针对同一基因组区域与类群集合的ARG云内各ARG的共同特征。本方法被命名为阈值共识法（threshold consensus），其判定规则为：仅当某基因组位点处存在该位点断点的ARG数量超过选定阈值时，才将该位点视作潜在的重组断点（recombination breakpoint）。后续通过两种方式进一步优化估计结果：一是忽略不会改变局部树拓扑结构（local tree topologies）的重组事件，二是合并仅由不变位点（invariant sites）分隔的断点位置。本研究采用谱系采样算法（genealogy sampling algorithm）推断的模拟ARG数据集，在一系列阈值参数下测试该阈值共识算法，并对最终生成的共识ARG的断点位置与局部树拓扑结构的准确性进行评估。