PhyloPhlAn

PhyloPhlAn is an integrated pipeline designed for large-scale phylogenetic profiling of genomes and metagenomes. It provides an accurate and rapid method for microbial genome characterization and phylogenetic analysis at multiple levels of resolution.

Key capabilities include:

• Assigning genomes and metagenome-assembled genomes (MAGs) to species-level genome bins (SGBs).
• Reconstructing strain-level phylogenies using clade-specific maximally informative phylogenetic markers.
• Scaling to very large phylogenies containing more than 17,000 microbial species.

You can install PhyloPhlAn by cloning the source repository and running the setup script. After installation, ensure that all required Dependencies and Tools are installed and available in your system path.

git clone https://github.com/biobakery/phylophlan
cd phylophlan
python setup.py install

The easiest way to install PhyloPhlAn is using the conda package manager from the bioconda channel.

conda install -c bioconda phylophlan

PhyloPhlAn provides several resources for learning how to use the pipeline, ranging from user manuals to specific biological use cases:

• User Manual: PhyloPhlAn User manual
• General Tutorials: PhyloPhlAn Tutorials
• Example 1: Phylogenetic characterization of isolate genomes of a given species (S. aureus)
• Example 2: Prokaryotes Tree of life reconstruction
• Example 3: Metagenomic analysis of the Ethiopian cohort
• Example 4: High-resolution phylogeny of genomes and MAGs of a known species (E. coli)
• Example 5: Phylogenetically characterization of an unknown SGB from the Proteobacteria phylum