recipe hyphy

An open-source software package for comparative sequence analysis using stochastic evolutionary models.

Homepage:

https://hyphy.org

Developer docs:

https://github.com/veg/hyphy

License:

MIT / MIT

Recipe:

/hyphy/meta.yaml

Links:

doi: 10.1093/molbev/msz197

HyPhy (Hypothesis Testing using Phylogenies) is an open-source software package for the analysis of genetic sequences (in particular the inference of natural selection) using techniques in phylogenetics, molecular evolution, and machine learning.

package hyphy

versions:

2.5.71-0,  2.5.70-0,  2.5.69-0,  2.5.65-1,  2.5.65-0,  2.5.64-1,  2.5.64-0,  2.5.63-0,  2.5.62-1, 

2.5.71-0,  2.5.70-0,  2.5.69-0,  2.5.65-1,  2.5.65-0,  2.5.64-1,  2.5.64-0,  2.5.63-0,  2.5.62-1,  2.5.62-0,  2.5.61-0,  2.5.60-1,  2.5.60-0,  2.5.59-0,  2.5.58-0,  2.5.57-0,  2.5.50-2,  2.5.50-1,  2.5.50-0,  2.5.49-0,  2.5.48-0,  2.5.47-0,  2.5.46-0,  2.5.42-0,  2.5.41-1,  2.5.41-0,  2.5.40-1,  2.5.40-0,  2.5.39-0,  2.5.38-0,  2.5.36-1,  2.5.36-0,  2.5.33-0,  2.5.32-0,  2.5.31-0,  2.5.30-1,  2.5.30-0,  2.5.29-1,  2.5.29-0,  2.5.28-0,  2.5.26-0,  2.5.25-0,  2.5.24-0,  2.5.23-0,  2.5.22.1-0,  2.5.22-0,  2.5.21-0,  2.5.20-0,  2.5.19-0,  2.5.17-0,  2.5.16-0,  2.5.15-0,  2.5.14-0,  2.5.12-1,  2.5.12-0,  2.5.11-0,  2.5.10-0,  2.5.9-0,  2.5.8-1,  2.5.8-0,  2.5.7-0,  2.5.6-0,  2.5.5-0,  2.5.4-1,  2.5.4-0,  2.5.3-0,  2.5.2-1,  2.5.2-0,  2.5.1-1,  2.5.1-0,  2.5.0-1,  2.5.0-0,  2.3.14-1,  2.3.14-0,  2.3.12-1,  2.3.12-0,  2.3.11-2,  2.3.11-1,  2.3.11-0

depends _openmp_mutex:

>=4.5

depends libcurl:

>=8.13.0,<9.0a0

depends libgcc:

>=13

depends libgomp:

depends libstdcxx:

>=13

depends libzlib:

>=1.3.1,<2.0a0

depends openmpi:

>=4.1.6,<5.0a0

requirements:

additional platforms:

linux-aarch64,  osx-arm64

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 hyphy

and update with::

   mamba update hyphy

To create a new environment, run:

mamba create --name myenvname hyphy

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/hyphy:<tag>

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

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