Supplementary data for paper "Anthropozoonotic spillovers reveal sustained long-term cryptic circulation of SARS-CoV-2 within and between Lithuanian mink farms"

This supplementary data includes BEAST output files, analysis code, and a limited sample metadata. The zipped folder "Beast_data" contains all files related to BEAST analyses.The subfolder "Log_and_history_trees_files" holds the raw BEAST output, including both used and discarded runs. The subfolder "Log_Combiner_output" contains post-burn-in combined files generated using LogCombiner v1.10.4. The subfolder "MCC_Trees" contains maximum clade credibility (MCC) trees created with TreeAnnotator v1.10.4 from post-burn-in history files. The subfolder "XML_files_no_alignment" contains XML files generated using BEAUti; sequence alignments have been removed from these files to comply with GISAID data-sharing policies. The folder "Code_and_metadata" contains code and additional data used in figure generation. The folders are named according to the image it was used to generate. A file titled Sample_table_with_EPI_ISL.csv provides the associated GISAID accession numbers. In some cases, exact matches were not possible as we have realinged the sequences and ended up with different consesus sequences, in such cases GISAID reference is added to "EPI_ISL_Sample_only" column. Also there are some mismathes due to the mislabeling of collection date during GISAID uploads. Some sequences are not available in GISAID. Contains file for GISAID aknowledgement, named "GISAID_acknowledgement_of_data_contributors.pdf" Contains a .fasta file with SARS-CoV-2 sequences originating from mink, realigned in our laboratory.