3. Relative rates sister-clades analysis

This folder contains the input and output files used in and obtained from the program Phyltest (Phyltest v.2.0, http://www.kumarlab.net/publications) for the sister-clade relative rates analysis. This folder is organised into subfolders by source study name and then by gene. The numbers at the beginning of the folder names do not have significance and are only used for organisational purposes. Transitions are identified by the set# in the file name (e.g. “Set1” or “S1” = transition #1, transitions as described in the Supplementary Material). All transitions were analysed with separate input and output files except for the transitions within the source study folder Cunha et al. 2011 where each transition was run from the same file per gene. Within the input files the abbreviations FL=flightless, F=flight-capable, OG=outgroup, and the number after these identifiers signifies the transition. Each gene folder (except where just described) contains 2 files per transition: 1 input file (nucleotide - “.dat”) and 1 output file.