recipe phylodeep

Deep-learning parameter estimation and model selection from phylogenetic trees.

Homepage:

https://github.com/evolbioinfo/phylodeep

Documentation:

https://github.com/evolbioinfo/phylodeep/blob/0.9/README.md

License:

GPL3 / GPL-3.0-or-later

Recipe:

/phylodeep/meta.yaml

PhyloDeep is a python library for parameter estimation and model selection from phylogenetic trees, based on deep learning.

package phylodeep

versions:

0.9-0,  0.7-0,  0.6-0

depends ete3:

>=3.1.1,<=3.1.3

depends keras:

2.2.4

depends matplotlib-base:

>=3.0.2,<3.7.0

depends pandas:

>=1.0.0,<1.4.0

depends phylodeep_data_bd:

>=0.6

depends phylodeep_data_bdei:

>=0.4

depends phylodeep_data_bdss:

>=0.4

depends python:

>=3.6

depends scikit-learn:

>=1.0,<1.3.0

depends tensorflow:

>=2.0.0

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 phylodeep

and update with::

   mamba update phylodeep

To create a new environment, run:

mamba create --name myenvname phylodeep

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/phylodeep:<tag>

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

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