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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.

MetaPhlAn documentation

MetaPhlAn 4

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

MetaPhlAn 3

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

MetaPhlAn2

A documentation for the previous version MetaPhlAn2 is available here

StrainPhlAn documentation

StrainPhlAn 4

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

StrainPhlAn 3

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

StrainPhlAn

A documentation for the first version of StrainPhlAn is available here

Strain Sharing Inference

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