I'm writing because I would like to suggest adding a backbone flag option to qiime2 phylogeny raxml-rapid-bootstrap. This would allow the user to build the tree not from scratch, but using this reference backbone tree as the initial structure. I apologize if I missed this, but cannot find it in the documentation or the tutorials as implemented thus far.
I am referring to Step 9 here: (constraint trees, backbone constraint): The Exelixis Lab, which seems to be the [-r] flag: raxmlHPC-SSE3 -p12345 -r backboneConstraint.txt. This allows you to provide a backbone tree where the backbone tree sequences and new study sequences are aligned together in order to add the new sequences to this well-defined backbone constraint tree structure.
q2-fragment-insertion could be a workaround, but ideally it would be great if this could be used with raxml to build trees. I hope you are able to add it as a flag in the next update-that would be amazing!