Supplementary data and scripts for Willemsen et al., 2019 "Genome plasticity in Papillomaviruses and de novo emergence of E5 oncogenes"

Supplementary data for Willemsen et al., 2019 "Genome plasticity in Papillomaviruses and de novo emergence of E5 oncogenes". The data set consists of three folders: “Alignments”, “Bali-Phy” and “RandomPermutationTests”. The “Alignments” folder contains the different alignments used for phylogenetic tree construction and comparison. The “Bali-Phy” folder contains the final results and convergence diagnostics of the Common Ancestry tests obtained by using the Bali-Phy software. The “RandomPermutationTests” folder contains all the data and scripts to repeat the random permutation tests described in the manuscript. Please see the corresponding README files for more information.