recipe pathphynder

A workflow for ancient DNA placement into reference phylogenies.

Homepage:

https://github.com/ruidlpm/pathPhynder

License:

MIT / MIT

Recipe:

/pathphynder/meta.yaml

Links:

doi: 10.1093/molbev/msac017

Ancient DNA data is characterized by deamination and low-coverage sequencing, which results in a high fraction of missing data and erroneous calls. These factors affect the estimation of phylogenetic trees with modern and ancient DNA, especially when dealing with many ancient samples sequenced to lower coverage. Furthermore, most ancient DNA analyses of the Y chromosome, for example, rely on previously known markers, but additional variation will continuously emerge as more data is generated. This workflow offers a solution for integrating ancient and present-day haploid data, first by identifiying informative markers in a high coverage dataset, second, by calling and filtering these SNPs in ancient samples and lastly, by traversing the tree and evaluate the number of derived and ancestral markers in the ancients to find the most likely branch where it belongs.

package pathphynder

(downloads) docker_pathphynder

versions:

1.2.3-0,  1.2.2-0,  1.2.1-3,  1.2.1-2,  1.2.1-1,  1.2.1-0,  1.2.0-0

depends phynder:

depends python:

depends r-base:

depends r-optparse:

depends r-phytools:

depends r-scales:

depends samtools:

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 pathphynder

and update with::

   mamba update pathphynder

To create a new environment, run:

mamba create --name myenvname pathphynder

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/pathphynder:<tag>

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

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