One of the things we used PhyloPhlAn 2 for was to predict the genus/species for new MAGs. This was output as a side product of placing MAGs in the tree of life, using the database of portein markers in the PhyloPhlAn database.
The new phylophlan_metagenomic script replaces this functionality, but it appears it can only use SGB databases. This gives us terrible resolution for our (rumen) MAGs, often going only to Phylum and sometimes to Family (but very very rarely to Genus or Species)
Is there a way of using phylophlan_metagenomic with the old protein biomarker database, so as to replicate the behaviour of PhyloPhlan2?
Alternatively, is there a way of asking PhyloPhlAn to output tabular taxonomy predictions when it places genomes in the tree of life?