:orphan:  .. only available via index, not via toctree

.. title:: Package Recipe 'phyml'
.. highlight: bash

phyml
=====

.. conda:recipe:: phyml
   :replaces_section_title:
   :noindex:

   Phylogenetic estimation using \(Maximum\) Likelihood

   :homepage: http://www.atgc-montpellier.fr/phyml/
   :documentation: https://github.com/stephaneguindon/phyml/blob/master/doc/phyml-manual.pdf
   
   :developer docs: https://github.com/stephaneguindon/phyml/
   :license: GPL / GPL-3.0-only
   :recipe: /`phyml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/phyml>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/phyml/meta.yaml>`_
   :links: biotools: :biotools:`phyml`, doi: :doi:`10.1093/sysbio/syq010`

   PhyML is a software that estimates maximum likelihood phylogenies from
   alignments of nucleotide or amino acid sequences. The main strength of
   PhyML lies in the large number of substitution models coupled to various
   options to search the space of phylogenetic tree topologies\, going from
   very fast and efficient methods to slower but generally more accurate
   approaches. PhyML was designed to process moderate to large data sets. In
   theory\, alignments with up to 4\,000 sequences 2\,000\,000 character\-long
   can be processed. PhyML can process data sets made of multiple genes and
   fit sophisticated substitution models with heterogeneous components
   across partition elements.



.. conda:package:: phyml

   |downloads_phyml| |docker_phyml|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>3.3.20220408-1</code>,  <code>3.3.20220408-0</code>,  <code>3.3.20211231-2</code>,  <code>3.3.20211231-1</code>,  <code>3.3.20211231-0</code>,  <code>3.3.20200621-2</code>,  <code>3.3.20200621-1</code>,  <code>3.3.20200621-0</code>,  <code>3.3.20190909-1</code>,  </span></summary>
      

      ``3.3.20220408-1``,  ``3.3.20220408-0``,  ``3.3.20211231-2``,  ``3.3.20211231-1``,  ``3.3.20211231-0``,  ``3.3.20200621-2``,  ``3.3.20200621-1``,  ``3.3.20200621-0``,  ``3.3.20190909-1``,  ``3.3.20190909-0``,  ``3.3.20190908-0``,  ``3.3.20190321-1``,  ``3.3.20190321-0``,  ``3.3.20180621-0``,  ``3.3.20170530-0``,  ``3.2.0-4``,  ``3.2.0-3``,  ``3.2.0-2``,  ``3.2.0-0``

      
      .. raw:: html

         </details>
      

   
   :depends libgcc-ng: ``>=12``
   :depends openmpi: ``>=4.1.5,<5.0a0``
   :requirements:

   .. rubric:: Installation

  You need a conda-compatible package manager
  (currently either `micromamba <https://mamba.readthedocs.io>`_, `mamba <https://mamba.readthedocs.io>`_, or `conda <https://docs.conda.io/projects/conda>`_)
  and the Bioconda channel already activated (see :ref:`set-up-channels`).

  While any of above package managers is fine, it is currently recommended to use either
  micromamba or mamba (see `here <https://mamba.readthedocs.io>`_ 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 phyml

   and update with::

      mamba update phyml

  To create a new environment, run::

      mamba create --name myenvname phyml

  with ``myenvname`` being a reasonable name for the environment
  (see e.g. the `mamba docs <https://mamba.readthedocs.io>`_ for details and further options).

  Alternatively, use the docker container::

      docker pull quay.io/biocontainers/phyml:<tag>

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


.. |downloads_phyml| image:: https://img.shields.io/conda/dn/bioconda/phyml.svg?style=flat
   :target: https://anaconda.org/bioconda/phyml
   :alt:   (downloads)
.. |docker_phyml| image:: https://quay.io/repository/biocontainers/phyml/status
   :target: https://quay.io/repository/biocontainers/phyml
.. _`phyml/tags`: https://quay.io/repository/biocontainers/phyml?tab=tags


.. raw:: html

    <script>
        var package = "phyml";
        var versions = ["3.3.20220408","3.3.20220408","3.3.20211231","3.3.20211231","3.3.20211231"];
    </script>






Download stats
-----------------

.. raw:: html
    :file: ../../templates/package_dashboard.html

Link to this page
-----------------

Render an |install-with-bioconda| badge with the following MarkDown::

   [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/phyml/README.html)

.. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat
   :target: http://bioconda.github.io/recipes/phyml/README.html