DHE calculation information from the<i> Marchantia </i>pangenome paper (https://doi.org/10.1038/s41588-024-02071-4)

This item contains scripts and datasets used to calculate Tajima's <i>D</i>, Fay and Wu's <i>H</i> and Zeng's <i>E</i> statistics on SNP data from <i>Marchantia polymorpha </i>(as well as on<i> A. thaliana</i> and<i> M. truncatula</i>). Folder M.polymorpha_file_processing contains scripts used to pre-process the SNP data, DHE_calculation_scripts contains the scripts to calculate <i>D</i>, <i>H</i> and <i>E</i> on unfolded SNP dataset (with ancestral allele known) and to calculate Tajima's <i>D</i> on the whole SNP dataset. The same calculations were also performed on<i> M. truncatula</i> and <i>A. thaliana</i> SNP data, downloaded at the links specified in the read_me_links file. The last folder contains vcf files of the outgroups used for the calculation on A. thaliana. Those VCFs were producted based on sequencing data from 30 <i>A. halleri</i> (PRJNA592307) and 29 <i>A. lyrata </i>(PRJNA357372), respectively mapped on the TAIR10 genome and for which polymorphic positions from the<i> A. thaliana</i> SNP dataset were called.