IQTree Documentation on Bootstrapping
To run a bootstrapping analysis in IQTree, we can use nearly the same command that we used to run a standard maximum likelihood tree search. We just add -b <NUM_BOOTSTRAP_REPLICATES> to the end of the command.
Return to the turtles data and run a nonparametric bootstrapping analysis on at least one dataset (concatenated or one of the individual genes) using a particular model.
If you have time, run multiple models and compare the results.