recipe phyling

A phylogenetic inference tool based on protein-coding genomic sequences

Homepage:

https://github.com/stajichlab/Phyling

Documentation:

https://github.com/stajichlab/Phyling/blob/v2.3.0/README.md

License:

MIT / MIT

Recipe:

/phyling/meta.yaml

Phyling is a fast, scalable, and user-friendly tool supporting phylogenomic reconstruction of species phylogenies directly from protein-encoded genomic data. It identifies orthologous genes by searching a sample's protein sequences against a Hidden Markov Models marker set, containing single-copy orthologs, retrieved from the BUSCO database. In the final step, users can choose between consensus and concatenation strategies to construct the species tree from the aligned orthologs.

package phyling

versions:

2.3.0-0

depends aster:

>=1.19

depends biopython:

>=1.81

depends clipkit:

>=2.1.1

depends fasttree:

>=2.1.1

depends iqtree:

>=2.4.0,<3.0

depends matplotlib-base:

>=3.5.3

depends muscle:

>=5.3

depends numpy:

>=2.0.2

depends phykit:

>=2.0.1

depends pyfaidx:

>=0.8.1.3

depends pyhmmer:

>=0.11.0

depends python:

>=3.9

depends raxml-ng:

>=1.2.2

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 phyling

and update with::

   mamba update phyling

To create a new environment, run:

mamba create --name myenvname phyling

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/phyling:<tag>

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

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