Steps needed to replicate the first phylogenetic analysis in TNT 1.5 (using the Dieudonne et al. 2021 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 traditional search (replications = 10000, hold = 10, and random seed = 0), with tree bisection reconnection (TBR) swapping algorithm

3. Second round of TBR branch swapping (bb;) applied to all trees retained in memory

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;)