How to construct the phylogenetic tree of the whole genus? I am confused about how to construct the phylogenetic tree of the streptomyces genus. The taxonomy of the streptomyces genus is mostly based on the MLST method, but now I need to use the gene data from NCBI to construct the phylogenetic tree of the streptomyces genus. Should I use the whole gene of the MLST's housekeeping gene to construct the tree? Or I should just use the loci to build the tree? Or the other method? I am a junior in university, have little knowledge of the filed., but my tutor asked me to do that. plus: Sorry for my awkward expression~
The MLST genes are not used to contruct a tree, because each pattern of alleles determines a predetermined genotype, e.g.  Staphlococcus aureus ST 22 is the MLST type concerning the MRSA epidemic. You could build a tree, but its only purpose is to visualise the ST, so its a bit pointless but okay at least you will not mistype something.

Performing a whole genome tree on Strep for the genus is complicated but doable and there are missing genes and stuff and if you just want typing then its not needed.



So if typing is your goal I would submit your MLST loci to the Steptomyces MLST database,

https://pubmlst.org/bigsdb?db=pubmlst_streptomyces_seqdef