recipe phylophlan

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes

Homepage:

https://github.com/biobakery/phylophlan

License:

MIT / MIT License

Recipe:

/phylophlan/meta.yaml

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.

package phylophlan

Versions:

3.0.3-0,  3.0.2-0,  3.0.1-0,  3.0-7,  3.0-6,  3.0-5,  3.0-4,  3.0-2,  3.0-1, 

3.0.3-0,  3.0.2-0,  3.0.1-0,  3.0-7,  3.0-6,  3.0-5,  3.0-4,  3.0-2,  3.0-1,  3.0-0

Depends:

• biopython >=1.73

• blast >=2.6.0

• dendropy >=4.4.0

• diamond >=0.9

• fasttree >=2.1.8

• iqtree >=1.6.6

• mafft >=7.310

• mash

• matplotlib-base >=3.1.0

• muscle >=3.8.1551

• numpy >=1.15.4

• pandas >=0.24.2

• python >=3.7

• raxml >=8.2.10

• seaborn >=0.9.0

• trimal >=1.4.1

Required By:

• metaphlan

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install phylophlan

and update with:

conda update phylophlan

or use the docker container:

docker pull quay.io/biocontainers/phylophlan:<tag>

(see phylophlan/tags for valid values for <tag>)

Download stats

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/phylophlan/README.html)