I need to construct a species tree for a plant pathogenic bacterial species which contains numerous pathovars in it. Since I have used AMPHORA tool and managed to extract 23 house keeping genes from 216 strains of the same and constructed species tree using RaxML with 100 bootstrap replicates and end up with very low bootstrap values because 70 percent of strains are identical to each other. I could not go for 16s rRNA based species tree because, I could not extract 16s rRNA sequences from most of the draft genomes. Therefore, I opted to go for SNP based species tree construction using CSI_SNP_Phylogeny, but here I have a problem regarding the out group organism incorporation. Since, CSI phylogeny need one reference genome and other strains genome whichever needed to be included. So, Can I include my outgroup organism as non-reference genomes in CSI server or I am following wrong procedure? Could anyone please guide me in this regard.
Thanks in advance!!!