I have produced a species table with Metaphlan3 but the level of classification is very low ~ 20%. This is expected due to the sample type which is not well studied.
I have assembled MAGs from the dataset and identified their taxonomy using Phylophlan. i.e. each assembled MAG can be identified as one of the SGBs in Phylophlan.
This brings the total level of classification up to 60%.
Is there a way to produce a species table which combined both of these results for me in Metaphlan3?
Many thanks in advance.