Question 1:
When I use Metaphlan4 reference database, I found that one categoryID (for example, UniRef90_A0A417FV47|1_4|SGB14991) corresponds to several bacteria species. I am confused about relative abundance of one bacteria specie calculated by Metaphlan4 when one bacteria specie and others all belong to one categoryID (one tategoryID means one sequence). Does that means reads counts of one sequence repetitively computate to get relative abundance of several bacteria species?
Question 2:
And, I download reference database from Index of /biobakery4/metaphlan_databases (unitn.it)
What is the role of each file in the figure?
If I haven’t posted my questions clearly, please let me know and I will add supplementary.
Thank you for your help!
Have a good day!