recipe bioconductor-scoup

Simulate Codons with Darwinian Selection Modelled as an OU Process

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/scoup.html

License:

GPL (>= 2)

Recipe:

/bioconductor-scoup/meta.yaml

An elaborate molecular evolutionary framework that facilitates straightforward simulation of codon genetic sequences subjected to different degrees and/or patterns of Darwinian selection. The model was built upon the fitness landscape paradigm of Sewall Wright, as popularised by the mutation-selection model of Halpern and Bruno. This enabled realistic evolutionary process of living organisms to be reproduced seamlessly. For example, an Ornstein-Uhlenbeck fitness update algorithm is incorporated herein. Consequently, otherwise complex biological processes, such as the effect of the interplay between genetic drift and mutation on the inference of diversifying selection, may now be investigated with minimal effort. Frequency-dependent and deterministic fitness landscape update techniques are also available.

package bioconductor-scoup

versions:

1.0.0-0

depends bioconductor-biostrings:

>=2.74.0,<2.75.0

depends r-base:

>=4.4,<4.5.0a0

depends r-matrix:

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 bioconductor-scoup

and update with::

   mamba update bioconductor-scoup

To create a new environment, run:

mamba create --name myenvname bioconductor-scoup

with myenvname being 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/bioconductor-scoup:<tag>

(see `bioconductor-scoup/tags`_ for valid values for ``<tag>``)

Download stats

Link to this page

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