MetaPhlAn 4 ignore_markers help

MetaPhlAn version 3.1.0

I am looking to exclude certain species from my metaphlan output. I can’t find any details about the --ignore-markers argument. Can I do this in a level that is more specific than kingdom? For example, how can I exclude any one of these levels: o__Enterobacterales|f__Enterobacteriaceae|g__Cronobacter|s__Cronobacter_universalis


Hi @jxx419
The metaphlan markers are defined at the species level, so removing all the markers (markers info file here: from the species of interest will do the job