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14.2 > Academic > MetaPhlAn2 (

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 (
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, 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)

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

This requires: msgpack-python, pandas, samtools-legacy, scipy, DendroPy, RAxML, biopython, muscle, ncbi-blast+, bowtie2, pysam, bcftools

Maintained by: Petar Petrov
Keywords: genomic shotgun,genomic,StrainPhlAn
ChangeLog: MetaPhlAn2


Source Downloads:
3a075f914593.tar.gz (956f8f6897a40e15cec38eb26cdcf97c)

Download SlackBuild:
MetaPhlAn2.tar.gz.asc (FAQ)

(the SlackBuild does not include the source)

Validated for Slackware 14.2

See our HOWTO for instructions on how to use the contents of this repository.

Access to the repository is available via:
ftp git cgit http rsync

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