”(Metagenomic Phylogenetic Analysis) MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. MetaPhlAn relies on unique clade-specific marker genes identified from 3,000 reference genomes…
The generation of this catalog of marker genes (marker catalog) uses an intraclade CDS clustering and then an extraclade sequence uniqueness assessment; the method was based loosely on our previous system for detecting core genes.It is an offline procedure that we perform regularly as a relevant set of newly sequenced microbial genomes is available, and the catalog is downloaded automatically with the associated classifier.
The MetaPhlAn classifier compares metagenomic reads against this precomputed marker catalog using nucleotide BLAST searches in order to provide clade abundances for one or more sequenced metagenomes.
…the MetaPhlAn classifier normalizes the total number of reads in each clade by the nucleo- tide length of its markers