metaphlan

Metagenomic Phylogenetic Analysis

Command lineScience

Not tested on a device yet. What that means

Commands in the package

metaphlan
add_metadata_tree.py
extract_markers.py
merge_metaphlan_tables.py
metaphlan2krona.py
plot_tree_graphlan.py
read_fastx.py
run_treeshrink.py
sample2markers.py
sgb_to_gtdb_profile.py
strain_transmission.py
strainphlan
treeshrink.py

About metaphlan

From Debian's package description

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

From Debian's description of the metaphlan package, under that package's license.

Dependencies

Depends on

python3-biom-format
python3-biopython
python3-dendropy
python3-h5py
python3-numpy
python3-pandas
python3-pysam
python3-requests
python3-scipy
python3
metaphlan2-data
python3-msgpack
python3-packaging
r-base-core
bowtie2

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Sources and licenses

Name: the Debian package name.
Summary: Debian's short description of the metaphlan package, under that package's license.
Description: Debian's description of the metaphlan package, under that package's license.
Versions and sizes: Debian's archive for ARM64, as on packages.debian.org.
Popularity: Debian Popularity Contest counts.