Hello Everyone,
I am analysing human oral microbes using metaphlan 4.0.6 and strainphlan also. I am funding on strain (t__) shared by multiple samples of my cohort and I would like to find other samples online sharing this same species in order to make a phylogenetic tree using Strainphlan. Thus, I wonder if there is a way to retrieve where this same species have been found in your article on metaphlan4 in other to dowload them.
Thanks a lot
Hi @Minuzzi
The t__ level does not represents strains but species-level genome bins (Redirecting). Unfortunatelly, in the paper we only reported the prevalence of the species not the single sample profiles.
Thank you @aitor.blancomiguez for your reply.
I have one more question: the marker fasta file obtained through
extract_markers.py
thus it represent the complete genome bin of that specifice species t__ indicated or it is just a fasta containing a number of markers (loci) able to identify that species?
thanks
Hi @Minuzzi
the extract_markers.py will get the FASTA file of the SGB-specific marker genes for the selected SGB