Steps needed to replicate the second phylogenetic analysis in TNT 1.5 (using the Madzia et al. 2018 matrix):



1. Increase number of trees that can be retained in memory to 100,000 (hold 100000;)

2. Tree search as described in the text using using new techonology algorithms: Driven search option for obtaining the trees (“Find minimum length 100 times”, and maintaining all other default parameters); for the search algorithms used, we enabled all four options: “Sectorial Search”, “Ratchet”, “Drift”, and “Tree fusing”. In the “Sectorial Search” settings, the number of drifting cycles used for selections of size above 75  was changed from 6 to 100, maintaining all other default parameters. In the “Ratchet” settings, the total number of iterations was changed from 10 to 100, maintaining all other default parameters. In the “Drift” settings, the number of cycles was changed from 10 to 100, maintaining all other default parameters. We did not alter the settings of the “Tree fusing” algorithm

4. Calculate the consistency and retention indices for the consensus tree using the script provided by TNT (stats.run;)

5. Generate Bremer support values (bsupport;)