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PhyloPhlAn\n\nPhyloPhlAn is an integrated pipeline for large-scale phylogenetic profiling of genomes and metagenomes.\nPhyloPhlAn is an accurate, rapid, and easy-to-use method for large-scale microbial genome characterization and phylogenetic analysis at multiple levels of resolution.\nPhyloPhlAn can assign both genomes and metagenome-assembled genomes (MAGs) to species-level genome bins (SGBs).\nPhyloPhlAn can reconstruct strain-level phylogenies using clade-specific maximally informative phylogenetic markers, and can also scale to very-large phylogenies comprising \u003e17,000 microbial species.\n\n# Installation\n\n## Bioconda\n\nYou can install PhyloPhlAn using conda as follows:\n\n~~~Bash\nconda install -c bioconda phylophlan\n~~~\n\n\n## Repository\n\nYou can clone the PhyloPhlAn repository from GitHub:\n\n~~~Bash\ngit clone https://github.com/biobakery/phylophlan\ncd phylophlan\npython setup.py install\n~~~\n\nThen remember to check that the [Dependencies and Tools](https://github.com/biobakery/phylophlan/wiki#requirements) are in stalled and available in your system.\n\n\n# Tutorials\n\n* [PhyloPhlAn User manual](https://github.com/biobakery/phylophlan/wiki)\n* [PhyloPhlAn Tutorials](https://github.com/biobakery/biobakery/wiki/PhyloPhlAn3)\n* [PhyloPhlAn Example 1: Phylogenetic characterization of isolate genomes of a given species (S. aureus)](https://github.com/biobakery/biobakery/wiki/PhyloPhlAn-3:-Example-01:-S.-aureus)\n* [PhyloPhlAn Example 2: Prokaryotes Tree of life reconstruction](https://github.com/biobakery/biobakery/wiki/PhyloPhlAn-3:-Example-02:-Tree-of-life)\n* [PhyloPhlAn Example 3: Metagenomic analysis of the Ethiopian cohort](https://github.com/biobakery/biobakery/wiki/PhyloPhlAn-3:-Example-03:-Metagenomic-application)\n* [PhyloPhlAn Example 4: High-resolution phylogeny of genomes and MAGs of a known species (E. coli)](https://github.com/biobakery/biobakery/wiki/PhyloPhlAn-3:-Example-04:-E.-coli)\n* [PhyloPhlAn Example 5: Phylogenetically characterization of an unknown SGB from the Proteobacteria phylum](https://github.com/biobakery/biobakery/wiki/PhyloPhlAn-3:-Example-05:-Proteobacteria)\n\n\n# Support\n\nWe provide support through [the bioBakery help forum](https://forum.biobakery.org/) and through the issues tracking system of the [PhyloPhlAn repository](https://github.com/biobakery/phylophlan/issues).\n\n\n# Citation\n\nIf you used PhyloPhlAn please cite the following paper:\n\n**Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0**  \n_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_  \nNat Commun 11, 2500 (2020)  \nDOI: [https://doi.org/10.1038/s41467-020-16366-7](https://doi.org/10.1038/s41467-020-16366-7)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiobakery%2Fphylophlan","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbiobakery%2Fphylophlan","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiobakery%2Fphylophlan/lists"}