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[ 源代码： metaphlan  ]

软件包：metaphlan（4.0.4+ds-1）

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Metagenomic Phylogenetic Analysis

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 newly added StrainPhlAn module, it is now possible to perform accurate strain-level microbial profiling.

MetaPhlAn relies on ~1.1M unique clade-specific marker genes (the latest marker information file mpa_v31_CHOCOPhlAn_201901_marker_info.txt.bz2 can be found here) 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

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