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MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. With the StrainPhlAn module, it is now possible to perform accurate strain-level microbial profiling.

MetaPhlAn documentation

MetaPhlAn 4

You can find here the documentation for the latest version (version 4) of MetaPhlAn.

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 (version 4) of StrainPhlAn.

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.