Produce species table which combines results of Metaphlan3 and MAGs whose taxonomy was defined using Phylophlan

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.

Hi @PeterCx
How did you assess the level of classification in your samples?