How to construct the phylogenetic tree of the whole genus?
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