PhyloPhlAn3
PhyloPhlAn is an integrated pipeline for large-scale phylogenetic profiling of genomes and metagenomes.
Most likely the easiest way to understand how you can use PhyloPhlAn in your analysis is to check out the examples below:
- Phylogenetic characterization of isolate genomes of a given species (S. aureus)
- Prokaryotes Tree of life reconstruction
- Metagenomic analysis of the Ethiopian cohort
- High-resolution phylogeny of genomes and MAGs of a known species (E. coli)
- Phylogenetic characterization of an unknown SGB from the Proteobacteria phylum
- Tutorial version: Metagenomic analysis of the Ethiopian cohort
Complementary files are available in the examples folder.
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
Nat Commun 11, 2500 (2020)
DOI: https://doi.org/10.1038/s41467-020-16366-7
