Method
1. Generate a diversified ensemble using the align command or super5 command.
2. Extract the MSA (M*) with highest column confidence using the maxcc command.
3. Create a resampled ensemble from the diversified ensemble using the resample command.
4. Estimate one tree for M* and one tree for every resampled replicate using your favorite phlyogenetic tree software.. Note that you can turn off bootstrapping in the tree software, because here we're going to make the tree ensemble ourselves. This will make estimating each tree much more efficient.
5. Calculate bootstrap values and make a new tree file using the newick conf command or RAxML support command.
Discussion
This procedure is regrettably clunky compared to standard bootstrapping, but there is no way to simplify it without integrating tree estimation into Muscle5 (or integrating Muscle5 into the tree software). With standard bootstrapping, the tree software can easily generate the MSA ensemble it needs from a single input MSA. With Muscle5 ensemble bootstrapping, each MSA is generated using different alignment parameters which tree software knows nothing about.
If you enable tree software bootstrapping for M*, this will enable you to compare standard bootstrap to the Muscle5 ensemble bootstrap.
