ARGs/trees inferred from Viridian data by sc2ts and UShER in tskit format

ARGs/trees inferred by sc2ts and UShER in tskit tree sequence format inferred from the Viridian SARS-CoV-2 dataset. The files are all provided in tszip format. To load the dataset into memory use: import tszip ts = tszip.load("sc2ts_viridian_v1.2.trees.tsz") The tskit Python API can then be used to process the data. There are four different variations here: sc2ts_viridian_v1.2.trees.tsz. Built from Viridian data up to 2023-02-21. Internal nodes have been dated using tsdate, and contains deletions and highly homoplasic sites post-hoc mapped on by parsimony. usher_viridian_v1.0.trees.tsz. Translation of the Viridian UShER tree to tskit format. Time units are uncalibrated and branch-lengths are not meaningful. sc2ts_viridian_inter_v1.2.trees.tsz. Subset of main sc2ts ARG subset to the intersection of samples and sites common to both the main sc2ts and UShER files above. Internal nodes have not been dated by tsdate and so will likely differ from the node dates on the main ARG. usher_viridian_inter_v1.2.trees.tsz. Subset of main UShER ARG subset to the intersection of samples and sites common to both. Internal nodes have been dated by tsdate.