Canid genealogies

Genealogies inferred using Relate (Speidel et al, Nature Genetics 2019) for canid genomes from the NHGRI Dog Genome Project comprising (722g, Plannais et al, Nature Communications 2019) and Dog10K project (Meadows et al Genome Biology 2023). These genealogies were analysed in an accompanying paper to uncover evolutinoary forces impacting the canine genome (bioRxiv). We additionally provide TMRCA estimates along the genome (tmrca.tgz) and mutation rate estimates for 96 triplet mutations (mutrates.tgz). This file also includes scripts to quantify relative mutation rates using Relate (e.g. in triplet contexts), as well as in low coverage ancient genomes. For ancient genomes, we ascertain for recent mutations in a genealogy to enrich for mutations associated with a pulse and divide the counts of mutation in some context (accounting for strand symmetry) with the number of mutations falling into the mutating single nucleotide category, e.g., CA/CT and TG/AG divided by A/T and T/A.