otoole et al (2023) apobec3 published data

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