recipe treetime

Maximum-Likelihood dating and ancestral inference for phylogenetic trees

Homepage:

https://github.com/neherlab/treetime

Documentation:

https://treetime.readthedocs.io/en/latest/index.html

License:

MIT / MIT

Recipe:

/treetime/meta.yaml

Links:

doi: 10.1093/ve/vex042

package treetime

versions:

0.11.4-0,  0.11.3-1,  0.11.3-0,  0.11.2-0,  0.11.1-0,  0.11.0-0,  0.10.1-0,  0.10.0-0,  0.9.6-0, 

0.11.4-0,  0.11.3-1,  0.11.3-0,  0.11.2-0,  0.11.1-0,  0.11.0-0,  0.10.1-0,  0.10.0-0,  0.9.6-0,  0.9.5-0,  0.9.4-0,  0.9.3-0,  0.9.2-0,  0.9.1-0,  0.9.0-0,  0.8.6-0,  0.8.5-0,  0.8.4-0,  0.8.3-0,  0.8.2-0,  0.8.1-0,  0.7.5-0,  0.7.4-1,  0.7.4-0,  0.7.3-0,  0.7.2-0,  0.7.0-0,  0.6.4.1-0,  0.6.3-0,  0.6.1-0,  0.5.6-0,  0.5.5-0,  0.5.3-0,  0.5.2-1,  0.5.2-0,  0.5.1-0,  0.5.0-0,  0.4.1-0,  0.4.0-0,  0.2.4-1,  0.2.4-0,  0.2.1-1,  0.2.1-0,  0.1-1

depends biopython:

>=1.67,!=1.77,!=1.78

depends matplotlib-base:

>=2.0

depends numpy:

>=1.10.4

depends pandas:

>=0.17.1

depends python:

>=3.7

depends scipy:

>=0.16.1

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 treetime

and update with::

   mamba update treetime

To create a new environment, run:

mamba create --name myenvname treetime

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/treetime:<tag>

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

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