Contents Data - 3 XML files (epoch model, exponential model and skygrid model with 2 APOBEC3 partitions defined). - 4 phylogenies (B.1 and Clade IIb, Clade I and Clade IIa, outgroup pruned) - 4 state reconstruction files (B.1 and Clade IIb, Clade I and Clade IIa) - 4 branch SNP reconstruction files (B.1 and Clade IIb, Clade I and Clade IIa) - 4 amino acid reconstruction files (B.1 and Clade IIb, Clade I and Clade IIa) - 4 snp count files (B.1 and Clade IIb, Clade I and Clade IIa) - 2 heptamer count files for Clade IIb (internal and all branches) - 4 root-to-tip data files (B.1 and Clade IIb, Clade I and Clade IIa) - 1 mutation count file including data from Clade IIb and B.1 Scripts - all_in_one notebook (notebook of most work from the paper- reconstructs the branch snps from the state files, generates tree figures, calculates amino acid information, calculates root-to-tip data for regression, code for generating figures present in the manuscript, sliding window calculations) - analysis_until_roottotip (stand alone notebook to get root-to-tip data) - cleaner_apobec_work (earlier version of analysis, including sankey diagram code) - get_ml_tree_with_reconstruction (shell commands for aligning, generating ml tree, reconstructing states and pruning off outgroup) - make_partitions (extraction of code for generating the two partitions of the alignment, apobec3 and non-apobec3) - roottotip.R (regression analysis using roottotip data) - synonprob.R (probability of getting x synonymous mutations given the data)