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

.. title:: Package Recipe 'bioconductor-pwalign'
.. highlight: bash

bioconductor-pwalign
====================

.. conda:recipe:: bioconductor-pwalign
   :replaces_section_title:
   :noindex:

   Perform pairwise sequence alignments

   :homepage: https://bioconductor.org/packages/3.20/bioc/html/pwalign.html
   :license: Artistic-2.0
   :recipe: /`bioconductor-pwalign <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-pwalign>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-pwalign/meta.yaml>`_

   The two main functions in the package are pairwiseAlignment\(\) and stringDist\(\). The former solves \(Needleman\-Wunsch\) global alignment\, \(Smith\-Waterman\) local alignment\, and \(ends\-free\) overlap alignment problems. The latter computes the Levenshtein edit distance or pairwise alignment score matrix for a set of strings.


.. conda:package:: bioconductor-pwalign

   |downloads_bioconductor-pwalign| |docker_bioconductor-pwalign|

   :versions:
      
      

      ``1.2.0-0``

      

   
   :depends bioconductor-biocgenerics: ``>=0.52.0,<0.53.0``
   :depends bioconductor-biocgenerics: ``>=0.52.0,<0.53.0a0``
   :depends bioconductor-biostrings: ``>=2.74.0,<2.75.0``
   :depends bioconductor-biostrings: ``>=2.74.0,<2.75.0a0``
   :depends bioconductor-iranges: ``>=2.40.0,<2.41.0``
   :depends bioconductor-iranges: ``>=2.40.0,<2.41.0a0``
   :depends bioconductor-s4vectors: ``>=0.44.0,<0.45.0``
   :depends bioconductor-s4vectors: ``>=0.44.0,<0.45.0a0``
   :depends bioconductor-xvector: ``>=0.46.0,<0.47.0``
   :depends bioconductor-xvector: ``>=0.46.0,<0.47.0a0``
   :depends libblas: ``>=3.9.0,<4.0a0``
   :depends libgcc: ``>=13``
   :depends liblapack: ``>=3.9.0,<4.0a0``
   :depends r-base: ``>=4.4,<4.5.0a0``
   :requirements:

   :additional platforms:
      
      .. raw:: html

         <span class="additional-platforms"><code>linux-aarch64</code></span>
      

   .. 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 bioconductor-pwalign

   and update with::

      mamba update bioconductor-pwalign

  To create a new environment, run::

      mamba create --name myenvname bioconductor-pwalign

  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/bioconductor-pwalign:<tag>

   (see `bioconductor-pwalign/tags`_ for valid values for ``<tag>``)


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


.. raw:: html

    <script>
        var package = "bioconductor-pwalign";
        var versions = ["1.2.0"];
    </script>






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

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

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