Package Recipe 'phylophlan'

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:

3.2.1-1, 3.2.1-0, 3.1.1-0, 3.1-0, 3.0.3-0, 3.0.2-0, 3.0.1-0, 3.0-7, 3.0-6,

3.2.1-1, 3.2.1-0, 3.1.1-0, 3.1-0, 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:

on biopython >=1.73
on blast >=2.6.0
on dendropy >=4.4.0
on diamond >=0.9
on fasttree >=2.1.8
on iqtree >=1.6.6
on mafft >=7.310
on mash
on matplotlib-base >=3.1.0
on muscle >=3.8.1551
on numpy >=1.15.4
on pandas >=0.24.2
on python >=3.9
on raxml >=8.2.10
on requests
on scipy
on seaborn >=0.9.0
on skani 0.2
on tqdm
on trimal >=1.4.1

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install phylophlan

to add into an existing workspace instead, run:

pixi add phylophlan

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install phylophlan

Alternatively, to install into a new environment, run:

conda create -n envname phylophlan

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

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

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

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)