MetaPhlAn2 is a computational tool for profiling the composition of
microbial communities (Bacteria, Archaea and Eukaryotes) from meta-
genomic shotgun sequencing data (i.e. not 16S) with species-level.

With the newly added StrainPhlAn module, it is now possible to perform
accurate strain-level microbial profiling. MetaPhlAn2 relies on ~1.5M
unique clade-specific marker genes. The latest marker information file
`mpa_v29_CHOCOPhlAn_201901_marker_info.txt.bz2` can be found in the
Download page (https://bitbucket.org/biobakery/metaphlan2/downloads/)
identified from ~100,000 reference genomes (~99,500 bacterial and
archaeal and ~500 eukaryotic), allowing:

* unambiguous taxonomic assignments;
* accurate estimation of organismal relative abundance;
* species-level resolution for bacteria, archaea, eukaryotes and viruses;
* strain identification and tracking
* orders of magnitude speedups compared to existing methods.
* metagenomic strain-level population genomics

If you use MetaPhlAn2, please cite:
MetaPhlAn2 for enhanced metagenomic taxonomic profiling. Duy Tin Truong,
Eric A Franzosa, Timothy L Tickle, Matthias Scholz, George Weingart,
Edoardo Pasolli, Adrian Tett, Curtis Huttenhower & Nicola Segata. Nature
Methods 12, 902-903 (2015)

If you use StrainPhlAn, please cite the MetaPhlAn2 paper and the
following StrainPhlAn paper:
Microbial strain-level population structure and genetic diversity from
metagenomes. Duy Tin Truong, Adrian Tett, Edoardo Pasolli, Curtis
Huttenhower, & Nicola Segata. Genome Research 27:626-638 (2017)

NOTE!
The script places the python files in /usr/share/MetaPhlAn2 and creates
symlinks to /usr/bin. If you are using metaphlan2.py with Ugene, it may
not work with the symlink. Instead, just point Ugene directly to
/usr/share/MetaPhlAn2/metaphlan2.py