I am interested in creating a phylogenetic tree of a portion of my rep-seqs (16S v 4) including reference sequences. Previously, I have been doing this probably an inefficiently and non-sensical manner that consisted of exporting my rep-seqs as a FASTA and using MEGA-X, adding in NCBI sequences of interest for reference, adding in an appropriate outgroup set of sequences and aligning it and then generating the ML tree (with bootstraps) and rooting it with the outgroup.
However, I have a feeling that this method probably does not make sense (maybe it does?). I conducted my taxonomic classification using a classifier trained with the SILVA138 database so theoretically is there anything wrong with using the SILVA database sequences as my reference sequences? I could be completely oblivious and maybe using mafft would already complete exactly what I need? Any guidance or input to help alleviate my confusion is greatly appreciated!