What's new in MetaPhlAn 3

New MetaPhlAn marker genes extracted with a newer version of ChocoPhlAn based on UniRef
Estimation of metagenome composed by unknown microbes with parameter --unknown_estimation
Automatic retrieval and installation of the latest MetaPhlAn database with parameter --index latest
Virus profiling with --add_viruses
Calculation of metagenome size for improved estimation of reads mapped to a given clade
Inclusion of NCBI taxonomy ID in the output file
CAMI (Taxonomic) Profiling Output Format included
Removal of reads with low MAPQ values

Provide feedback