Through an RNA seq approach, I have identified 356 single copy orthologous groups across 9 species for their phylogenetic analysis. I now want construct species based phylogenetic tree.
What shall I do? Shall I merge all the genes of a species into a single super gene and do this for all species and then proceed for tree construction or not? How feasible and good it is.
If I simply use the individual genes of each species, I get a gene tree and not species tree.