MetaPhlAn2 (METAgenomic PHyLogenetic ANalysis) is a tool for profiling the composition of microbial communities (bacteria, archaea, eukaryotes, and viruses) from whole-metagenome shotgun sequencing data.

Element type: metaphlan2-classify


ParameterDescriptionDefaultvalueParameter in Workflow FileType
Input data

To classify single-end (SE) reads or contigs, received by reads de novo assembly, set this parameter to "SE reads or contigs".

To classify paired-end (PE) reads, set the value to "PE reads".

SE reads or contigs



Input file format

Set type of an input file (--input-type). Each input file will usually contain a lot of sequences that should be classified.





A path to a folder with MetaPhlAn2 database: BowTie2 index files, built from reference genomes, and *.pkl file (--mpa-pkl, --bowtie2db).

By default, "mpa_v20_m200" database is provided (if it has been downloaded). The database was built on ~1M unique clade-specific marker genes identified from ~17,000 reference genomes (~13,500 bacterial and archaeal, ~3,500 viral, and ~110 eukaryotic).



Number of threads

The number of CPUs to use for parallelizing the mapping (--nproc).




Analysis type

Specify the type of analysis to perform:

  • Relative abundance - profiling of metagenomes in terms of relative abundances (corresponds to "-t rel_ab")
  • Relative abundance with reads statistics - profiling of metagenomes in terms of relative abundances and estimate the number of reads coming from each clade ("-t rel_ab_w_read_stats")
  • Reads mapping - mapping from reads to clades, the output contains reads that hit a marker only ("-t reads_map")
  • Clade profiles - normalized marker counts for clades with at least a non - null marker("-t clade_profiles")
  • Marker abundance table - normalized marker counts: only when > 0.0 and optionally normalized by metagenome size ("-t marker_ab_table"), see also "Normalize by metagenome size" parameter
  • Marker presence table - list of markers present in the sample ("-t marker_pres_table"), see also "Presence threshold" parameter

Relative abundance



Tax levelThe taxonomic level for the relative abundance output: all, kingdoms (Bacteria and Archaea) only, phyla only, etc. (--tax_lev).All 



Bowtie2 output fileThe file for saving the output of BowTie2 (--bowtie2out). In the case of PE reads one file is created per each pair of files.Auto 



Output fileMetaPhlAn2 output depends on the "Analysis type" parameter. By default, it is a tab-delimited file with the predicted taxon relative abundances.Auto 



Normalize by metagenome sizeThe parameter is present only when "Analysis type" is equal to "Marker abundance table". It is a combo box with values "Skip" (default) and "Normalize". If "Normalize" is selected, the total number of reads in the original metagenome is taken into account for normalization: UGENE calculates the number of reads in an input FASTA/FASTQ file and passes "--nreads" parameter to MetaPhlAn2.
Presence thresholdThe parameter is present only when "Analysis type" is equal to the "Marker presence table". It is an INT value >= 0. The default value is 1. Specify a threshold for calling a marker.

Input/Output Ports

The element has 1 input port:

Name in GUI: Input sequences

URL(s) to FASTQ or FASTA file(s) should be provided. In the case of SE reads or contigs use the "Input URL 1" slot only. In case of PE reads input "left" reads to "Input URL 1", "right" reads to "Input URL 2".See also the "Input data" parameter of the element

Name in Workflow File: in


SlotInGUISlot in Workflow FileType
Input URLurlstring