- recipe alleleflux
A tool for fine-grained evolutionary analysis of microbial populations and communities
- Homepage:
- Documentation:
- License:
GPL3 / GPL-3.0-or-later
- Recipe:
AlleleFlux is a python package for analyzing allele frequencies trajectories in metagenomic data. It profiles MAG (Metagenome-Assembled Genome) populations across samples, detecting parallel evolution through allele frequency changes.
- package alleleflux¶
- versions:
0.1.14-0,0.1.4-0- depends biopython:
- depends click:
- depends intervaltree:
- depends matplotlib-base:
- depends numpy:
- depends pandas:
- depends pysam:
- depends python:
>=3.9- depends pyyaml:
- depends questionary:
- depends r-base:
- depends r-tidyr:
- depends rpy2:
- depends scipy:
- depends seaborn:
- depends snakemake-executor-plugin-cluster-generic:
- depends snakemake-minimal:
>=8.0.0- depends statsmodels:
- depends tqdm:
- requirements:
- additional platforms:
Installation
You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install alleleflux and update with:: mamba update alleleflux
To create a new environment, run:
mamba create --name myenvname alleleflux
with
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).Alternatively, use the docker container:
docker pull quay.io/biocontainers/alleleflux:<tag> (see `alleleflux/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/alleleflux/README.html)
