You can submit a protein sequence if the species you are studying is not represented in the PhyloGenes precomputed gene families (check the full species list here). The TreeGrafter [Tang2019] tool will run hmm scoring and find the best matching gene family, add your sequence to the MSA of that family, then run RAxML to insert your sequence to the best location of the gene family tree. Your sequence will be labeled as 'grafted'.
There are two entry places to take you to the protein sequence input box:
An example grafted tree:
