Relate-inferred genealogies for 66 longread Arabidopsis thaliana genomes
Creators
- 1. University of Toronto
- 2. University of California - Davis
Description
Relate-inferred genealogies for 66 longread Arabidopsis thaliana genomes.
The genomes are the samples used in Wlodzimierz et al. 2023 (https://doi.org/10.1038/s41586-023-06062-z).
longread-trees.tar.gz contains the output of Relate's estimate population size command (https://myersgroup.github.io/relate/modules.html#CoalescenceRate), including an anc/mut/dist/coal file for every chromosome. It also constains a tskit tree sequence (https://tskit.dev/) for each chromosome, converted from anc/mut.
Thal_ref_Boec_Lyra_Malc_outgroups_nodupes_orthoonly.maf 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.
Snakefile is the code we used to generate the genealogies.
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