MetaPhlAn Versions Save

MetaPhlAn 3.1 represents a moderate update to the bioBakery 3 software and databases. This update is based on improvements in our ability to align NCBI-sourced microbial genomes and their constituent genes to UniProt resources alongside additional removal of low-quality species (see PMID:33944776 for the definition of “low-quality species”).

What has changed in version 3.1:

• 433 low-quality species were removed from the MetaPhlAn 3.1 marker database and 2,680 species were added (for a new total of 15,766; a 17% increase).
• Marker genes for a subset of existing bioBakery 3 species were also revised.
• Most existing bioBakery 3 species pangenomes were updated with revised or expanded gene content.
• MetaPhlAn 3.1 software has been updated to work with revised marker database.