Package: metaphlan2 (2.7.8-1)

[ Source: metaphlan2  ]

Metagenomic Phylogenetic Analysis

MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution. From version 2.0, MetaPhlAn is also able to identify specific strains (in the not-so-frequent cases in which the sample contains a previously sequenced strains) and to track strains across samples for all species.

MetaPhlAn 2.0 relies on ~1M unique clade-specific marker genes (the marker information file can be found at usr/share/metaphlan2/utils/markers_info.txt.bz2) identified from ~17,000 reference genomes (~13,500 bacterial and archaeal, ~3,500 viral, and ~110 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

Other Packages Related to metaphlan2

• dep: bowtie2

  ultrafast memory-efficient short read aligner

• dep: metaphlan2-data

  data package for Metagenomic Phylogenetic Analysis

• dep: python

  interactive high-level object-oriented language (Python2 version)

• dep: python-biom-format

  Biological Observation Matrix (BIOM) format (Python 2)

• dep: python-msgpack

  Python implementation of MessagePack format

• dep: python-pandas

  data structures for "relational" or "labeled" data

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