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Precise phylogenetic analysis of microbial isolates and genomes from metagenomes
Python Perl Shell
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PhyloPhlAn 3.0 is an integrated pipeline for large-scale phylogenetic profiling of genomes and metagenomes. PhyloPhlAn 3.0 is an accurate, rapid, and easy-to-use method for large-scale microbial genome characterization and phylogenetic analysis at multiple levels of resolution. PhyloPhlAn 3.0 can assign both genomes and metagenome-assembled genomes (MAGs) to species-level genome bins (SGBs). PhyloPhlAn 3.0 can reconstruct strain-level phylogenies using clade-specific maximally informative phylogenetic markers, and can also scale to very-large phylogenies comprising >17,000 microbial species.



You can install PhyloPhlAn using conda as follows:

conda install -c bioconda phylophlan


You can clone the PhyloPhlAn repository from GitHub:

git clone
cd phylophlan
python install

Then remember to check that the Dependencies and Tools are in stalled and available in your system.



We provide support through the bioBakery help forum and through the issues tracking system of the PhyloPhlAn repository.


If you used PhyloPhlAn please cite the following paper:

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0
Francesco Asnicar, Andrew Maltez Thomas, Francesco Beghini, Claudia Mengoni, Serena Manara, Paolo Manghi, Qiyun Zhu, Mattia Bolzan, Fabio Cumbo, Uyen May, Jon G. Sanders, Moreno Zolfo, Evguenia Kopylova, Edoardo Pasolli, Rob Knight, Siavash Mirarab, Curtis Huttenhower, and Nicola Segata
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