It would be good to have a "bootstrap" function to run after the de novo workflow to allow generation of bootstrapped trees. The code for this already exists in the GenomeTreeTk, but it would be good to have this in the GTDB-Tk itself. Also, we should change the default tree to be inferred WITHOUT the GAMMA model since we are moving away from this. A "--gamma" flag should then be added to let people use this model is desired.
It would be good to have a "bootstrap" function to run after the de novo workflow to allow generation of bootstrapped trees. The code for this already exists in the GenomeTreeTk, but it would be good to have this in the GTDB-Tk itself. Also, we should change the default tree to be inferred WITHOUT the GAMMA model since we are moving away from this. A "--gamma" flag should then be added to let people use this model is desired.