You can submit a protein sequence if If the species you are studying is not represented in the PhyloGenes precomputed gene families (check the full species list here), you can submit an individual protein sequence and 'graft' the sequence onto existing precomputed gene families. The TreeGrafter [Tang2019] tool will run hmm 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'.
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