recipe metaclock

A python package for facilitating strain-level phylogenetic and molecular clock analysis



A-GPL 3.0



package metaclock

(downloads) docker_metaclock



depends biopython:

depends blast:


depends bowtie2:

depends bzip2:

depends cmseq:

depends dendropy:

depends ete3:

depends mapdamage2:

depends matplotlib-base:

depends numpy:

depends perl-bioperl:

depends prokka:

depends pysam:

depends python:


depends raxml:

depends samtools:

depends scikit-learn:

depends seaborn:

depends trimal:



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 metaclock

and update with::

   mamba update metaclock

To create a new environment, run:

mamba create --name myenvname metaclock

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<tag>

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

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