Dsuite - fast D-statistics and related admixture evidence from VCF files
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Patterson’s D, also known as the ABBA-BABA statistic, and related statistics such as the f4-ratio, are commonly used to assess evidence of gene flow between populations or closely related species. Currently available implementations often require custom file formats, implement only small subsets of the available statistics, and are impractical to evaluate all gene flow hypotheses across datasets with many populations or species due to computational inefficiencies. Here we present a new software package Dsuite, an efficient implementation allowing genome scale calculations of the D and f4-ratio statistics across all combinations of tens or hundreds of populations or species directly from a variant call format (VCF) file. Our program also implements statistics suited for application to genomic windows, providing evidence of whether introgression is confined to specific loci and it can also aid in interpretation of a system of f4-ratio results with the use of the ‘f-branch’ method. Dsuite is available at https://github.com/millanek/Dsuite, is straightforward to use, substantially more computationally efficient than comparable programs, and provides a convenient suite of tools and statistics, including some not previously available in any software package. Thus, Dsuite facilitates the assessment of evidence for gene flow, especially across larger genomic datasets.
帕特森D统计量（Patterson’s D，又称ABBA-BABA统计量）以及诸如f4-ratio等相关统计量，是评估种群或近缘物种间基因流证据的常用工具。当前已有的实现方案通常要求使用自定义文件格式，仅支持部分可用统计量的计算，且由于计算效率低下，难以在包含数十乃至数百个种群或物种的数据集上全面验证所有基因流假说。本文推出一款全新的软件包Dsuite，其可高效地直接从变异调用格式（Variant Call Format, VCF）文件中，对数十乃至数百个种群或物种的所有组合开展全基因组范围的D统计量与f4-ratio统计量计算。该程序还实现了适用于基因组窗口的统计方法，可用于判断基因渐渗是否局限于特定位点；同时借助"f-branch"方法，还能辅助解读f4-ratio统计结果。Dsuite的开源地址为https://github.com/millanek/Dsuite，其操作简便，计算效率远优于同类软件，并提供了一套便捷的工具与统计量集合，其中部分统计量此前尚未在任何软件包中出现。综上，Dsuite能够有效助力基因流证据的评估，尤其适用于大型基因组数据集的相关分析。
