Data-set empirical trees

The input file” treebase_input.rda” has the trees cached from TreeBase by the R-package treebase (Sanderson, M.J., Donoghue, M.J., et al. 1994). The file was later treated for specific statistics and compared with simulated trees, as described in out methodology. For that the “processing_treebase.R” R-script was used, being the file “treebaselist_output.RData” the final output. We would like to stress that this is not a complete catalogue of all R-scripts used in our study, especially regarding plotting and investigation of model behavior, once much was simulated with a cluster computer involving multiple outputs, code files and csv parameter tables that changed over time. If you plan to run similar experiments, we strongly encourage the reading of our TreeSimGM R-package help material.