Denmark SARS-CoV-2 phylogenetic intermediates: bootstrap topologies, time-trees and BEAST2 trees for the STEPHY application

Phylogenetic artefacts underlying the empirical application of STEPHY to SARS-CoV-2 transmission between the five Danish regions during 2021. For each of the Alpha, Delta and Omicron variants: 40 standard non-parametric bootstrap topologies plus one maximum-likelihood topology from IQ-TREE, the corresponding time-calibrated trees and node data from augur refine, division ancestral-state reconstructions from augur traits, and per-clade MRCA summaries. Also included are the 205 BEAST2 NEXUS tree files (five Nextstrain clades × 41 trees) that are fed directly to STEPHY.