Skip to content
Precise phylogenetic analysis of microbial isolates and genomes from metagenomes
Python Perl Shell
Branch: master
Clone or download

Latest commit

Latest commit 2b37436 Mar 31, 2020

Files

Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
phylophlan updating call to phylophlan_write_default_configs.sh Mar 31, 2020
recipe updating meta.yaml Mar 31, 2020
.gitignore gitignore up Mar 10, 2020
license.txt auto-detection of db_type, adding other minor fixings, start cleaning… Mar 15, 2018
readme.md adding citation Mar 26, 2020
setup.py updating call to phylophlan_write_default_configs.sh Mar 31, 2020

readme.md

PhyloPhlAn

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.

Installation

Bioconda

You can install PhyloPhlAn using conda as follows:

conda install -c bioconda phylophlan

Repository

You can clone the PhyloPhlAn repository from GitHub:

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

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

Tutorials

Support

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

Citation

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
In review

You can’t perform that action at this time.