Relate-inferred genealogies for 1552 Arabidopsis thaliana samples

Relate-inferred genealogies for 1552 Arabidopsis thaliana samples.

The genealogies for each of the 5 autosomes are given as .anc.gz and .mut.gz files.

Each chromosome also has a .dist and .coal file, giving the space between mutations (accounting for genomic mask) and the inferred coalescence rates (inferred from trees on that chromosome only for the sake of computation time).

keep.poplabels gives the IDs of the samples, in the order given to Relate. Since we filter out heterozygous sites, there is only one sample for each diploid individual.

Pipeline given in Snakefile with Python environment given in requirements.txt.

Genetic data from Durvasula et al 2017 (https://www.pnas.org/doi/abs/10.1073/pnas.1616736114), https://www.ebi.ac.uk/ena/browser/view/PRJEB44201?show=analyses.

The .maf file is the multi-species alignment (kindly provided by Tyler Kent, Adrian Platts, and the Brassicales Map Alignment Project (DOE-JGI, http://bmap.jgi.doe.gov/)) that we used to polarize the alleles.

Please don't hesitate to get in touch with questions.

Matt