MetaPhlAn is a computational tool for species-level microbial profiling (bacteria, archaea, eukaryotes, and viruses) from metagenomic shotgun sequencing data. StrainPhlAn (available within MetaPhlAn) allows strain-level microbial population genomics.

You can find here the documentation for the latest version of MetaPhlAn (v4.1). The documentation for version 4.0 is also available here.

You can find here the documentation for the 3.1 version of MetaPhlAn. The documentation for version 3.0 is also available here.

A documentation for the previous version MetaPhlAn2 is available here

You can find here the documentation for the latest version of StrainPhlAn (v4.1). The documentation for version 4.0 is also available here.

You can find here the documentation for the 3 version of StrainPhlAn.

A documentation for the first version of StrainPhlAn is available here

You can find here the documentation for performing strain sharing analyses using StrainPhlAn.