It seems StrainPhlAn only report one strain of each species for each sample according to the Bacteroides caccae example and the StrainPhlAn paper. Is that possible to obtain multiple conspecific strains for each sample using StrainPhlAn? Thanks a lot.
Hi Zhixing, thanks for getting in touch
No, StrainPhlAn returns the genetic profiles (i.e. marker sequences) of the most abundant (dominant) strain for each species. So you do the population genetic analysis across samples you are comparing the dominant strains in the population. StrainPhlAn discards the cases in which two strains from the same species are at the same abundance as it is not possible to assign the SNPs to one or the other.