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Dsuite - fast D-statistics and related admixture evidence from VCF files

By Milan Malinsky, Michael Matschiner, Hannes Svardal

Posted 10 May 2019
bioRxiv DOI: 10.1101/634477 (published DOI: 10.1111/1755-0998.13265)

1. Patterson’s D , also known as the ABBA-BABA statistic, and related statistics such as the f 4-ratio, are commonly used to assess evidence of gene flow between populations or closely related species. Currently available implementations require custom file formats and are impractical to evaluate all gene flow hypotheses across datasets with many populations or species. 2. Dsuite is a fast C++ implementation, allowing genome scale calculations of the D and f 4-ratio statistics across all combinations of tens or hundreds of populations or species directly from a variant call format (VCF) file. Furthermore, the program can provide evidence of whether introgression is confined to specific loci and aid in interpretation of a system of f 4-ratio results by implementing the ‘f-branch’ method. 3. Dsuite is available at <https://github.com/millanek/Dsuite>, is straightforward to use, substantially more computationally efficient than other comparable programs, and presents a novel suite of tools and statistics, including some not previously available in any software package. 4. Thus, Dsuite facilitates assessment of evidence for gene flow, especially across large genomic datasets.

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