recipe bioconductor-sitepath

Phylogeny-based sequence clustering with site polymorphism

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/sitePath.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-sitepath/meta.yaml

Using site polymorphism is one of the ways to cluster DNA/protein sequences but it is possible for the sequences with the same polymorphism on a single site to be genetically distant. This package is aimed at clustering sequences using site polymorphism and their corresponding phylogenetic trees. By considering their location on the tree, only the structurally adjacent sequences will be clustered. However, the adjacent sequences may not necessarily have the same polymorphism. So a branch-and-bound like algorithm is used to minimize the entropy representing the purity of site polymorphism of each cluster.

package bioconductor-sitepath

versions:

1.18.0-0,  1.16.0-0,  1.14.0-1,  1.14.0-0,  1.10.2-1,  1.10.2-0,  1.10.0-0,  1.8.0-0,  1.6.3-0, 

1.18.0-0,  1.16.0-0,  1.14.0-1,  1.14.0-0,  1.10.2-1,  1.10.2-0,  1.10.0-0,  1.8.0-0,  1.6.3-0,  1.6.0-0,  1.4.0-0,  1.2.1-0,  1.0.2-0

depends bioconductor-ggtree:

>=3.10.0,<3.11.0

depends bioconductor-ggtree:

>=3.10.0,<3.11.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends r-ape:

depends r-aplot:

depends r-base:

>=4.3,<4.4.0a0

depends r-ggplot2:

depends r-ggrepel:

depends r-gridextra:

depends r-rcolorbrewer:

depends r-rcpp:

depends r-seqinr:

depends r-tidytree:

requirements:

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-sitepath

and update with::

   mamba update bioconductor-sitepath

To create a new environment, run:

mamba create --name myenvname bioconductor-sitepath

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-sitepath:<tag>

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

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