Supplementary data and scripts for Willemsen and Bravo, 2020 "Ecological opportunity, radiation events and genomic innovations shaped the episodic evolutionary history of papillomaviruses".

Supplementary data and scripts for Willemsen and Bravo, 2020 "Ecological opportunity, radiation events and genomic innovations shaped the episodic evolutionary history of papillomaviruses". The data set consists of four folders: “alignments”, "RScripts_and_inputData", "startingTrees" and “xml_files”. The “alignments” folder contains the Gblocks filtered and subsequently concatenated E1-E2-L2-L1 alignments used for phylogenetic tree construction. For each data set (RD1, RD2, FD and FDF), alignments are provided in fasta and in nexus format. The "RScripts_and_inputData" folder contains the R scripts and corresponding input data used for performing statistical analyses. This folder contains sub-folders organised by Figure numbers. The "startingTrees" contains the nexus files of the starting trees that were used for phylogenetic reconstruction. The “xml_files” folder contains xml files used for phylogenetic time inference. For each data set, one xml file is given per clock and tree model tested.