Data 1 for: The molecular epidemiology of multiple zoonotic transmissions of SARS-CoV-2

Data for "The molecular epidemiology of multiple zoonoses of SARS-CoV-2". 

The data is separated into several outputs:

1. BEAST XML files and outputs. The BEAST XML files have had sequences removed; they need to be downloaded, aligned, and placed in appropriately to run the XML files. 

2. The reversion analysis includes the Main Text and supplemental global trees with reversions. 

3. The sarbecovirus nonrecombinant region trees directory includes the trees generation from the nonrecombinant regions and recCA. 

4. The simulation outputs for the primary analysis are provided (these are available in Data 2-5, DOIs below); instructions for generating simulations are available at the Github associated with the paper. The simulations_XX.zip files are the 1100 successful simulation outputs; the simulations_pooled_results.zip file includes the pooled simulation results, which are then used for rejection sampling. 

5. The rejection sampling includes all the rejection sampling results; details on usage can be found at the Github associated with the paper. Make sure each of the rejection sampling files (rejection_sampling_primaryAnalysis.z01, rejection_sampling_primaryAnalysis.z02, and rejection_sampling_primaryAnalysis.zip) are downloaded and in the same directory when trying to unzip them. There should be a single resulting unzipped directory. 

6. The cumulative simulations results, which are essentially pooled results of the primary simulations. These results include (a) the pooled FAVITES-COVID-Lite results (e.g., the time of stable coalescence for each simulation), (b) the combined GEMF results for successful simulations, for either daily infection counts or cumulative infection counts, (c) the combined GEMF results for failed simulations, for either daily infection counts or cumulative infection counts, and (d) the phylogenetic structure results, detailing the number of descending 1- or more mutation clades (clade_analysis_CC) or 2-mutation clades (clade_analysis_AB). There are notebooks available through the Code submission associated with the manuscript that can be used to analyze these files, including calculating statistics and plotting figures. 

The simulation outputs are available at Data 2-5: 

Data 2: https://doi.org/10.5281/zenodo.6887142

Data 3: https://doi.org/10.5281/zenodo.6887149

Data 4: https://doi.org/10.5281/zenodo.6887155

Data 5: https://doi.org/10.5281/zenodo.6887170