I need to construct the phylogenetic tree of the whole genus of streptomyces. And my goal is to find out how my target strep species distributed in the whole strep genus and obtain the distribution pattern. Strep is a big genus, has 658 species(65% of them have the genome info), and my target species is about 25. But the traditional 16S method seems not helping when it comes to strep is a genetic recombination genus. And still lack of MLST scheme to distinguish my target species. I want to get the phylogeny for the whole genus, but I lack related genetics knowledge.
There is something I did before try to get the tree.
- I ran the orthomcl program for 400 strep genomes which I got from NCBI, and the result is: I got 22 orthologues
- I ran the fastani program for 200 strep genomes(type material) and got the ani result.
What can I do to achieve my goal? Thanks!