recipe phynder

Efficient likelihood calculations to place samples into a phylogenetic tree.

Homepage:

https://github.com/richarddurbin/phynder

License:

MIT / MIT

Recipe:

/phynder/meta.yaml

Efficient likelihood calculations to place samples into a phylogenetic tree. In particular, phynder was originally designed for placing male ancient DNA samples into the Y chromosome phylogeny, when there are arbitrarily high rates of missing data. It has also been used for assigning ancient samples to whole mitochondrial genome phylogenies.

package phynder

(downloads) docker_phynder

versions:

1.0-4,  1.0-3,  1.0-2,  1.0-1,  1.0-0

depends bzip2:

>=1.0.8,<2.0a0

depends libcurl:

>=8.11.1,<9.0a0

depends libdeflate:

>=1.22,<1.23.0a0

depends libgcc:

>=13

depends liblzma:

>=5.6.3,<6.0a0

depends libzlib:

>=1.3.1,<2.0a0

depends openssl:

>=3.4.0,<4.0a0

requirements:

additional platforms:
linux-aarch64

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 phynder

and update with::

   mamba update phynder

To create a new environment, run:

mamba create --name myenvname phynder

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/phynder:<tag>

(see `phynder/tags`_ for valid values for ``<tag>``)

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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