This folder contains all files used for the phylogenetic analysis presented in this manuscript.

Folder contents:

1. ML_Tempest: 
-Tree file: IqTree Maximum Likelihood tree of the 1,182 genomes used in this study.
-Txt file: TempEst root-to-tip regression data.

2. MolClock:
-Exponential.xml: xml file with all the information used for the BEAST run of the 1,182 SARS-CoV-2 sequences used in this study under an exponential coalescent model.
-Skygrid.xml: xml file with all the information used for the BEAST run of the 1,182 SARS-CoV-2 sequences used in this study under a skygrid coalescent model.

3. Pangolin:
-Brazil_Pangolin.csv: output file of the lineage assignment analysis performed using Pangolin.

4. Phylogeography:
-Continuous: Script, xml and metadata used for the continuous phylogeopgraphic analysis presented in Figures 4a and b.
-Discrete: Empirical trees, xml and metadata used for the discrete phylogeopgraphic analysis presented in this study.

