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bioRxiv · 10.1101/634477

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

Malinsky, M.
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Abstract

O_LIPattersons 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 require custom file formats and are impractical to evaluate all gene flow hypotheses across datasets with many populations or species. C_LIO_LIDsuite is a fast C++ 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. Furthermore, the program can provide evidence of whether introgression is confined to specific loci and aid in interpretation of a system of f4-ratio results by implementing the f-branch method. C_LIO_LIDsuite 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. C_LIO_LIThus, Dsuite facilitates assessment of evidence for gene flow, especially across large genomic datasets. C_LI

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Malinsky, M.. 2019-05-10. Dsuite - fast D-statistics and related admixture evidence from VCF files. https://doi.org/10.1101/634477

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