API Reference
=============

.. toctree::
   :hidden:

   Alignment <alignment>
   Trimmers <trimmer>
   Similarity Matrix <similarity_matrix>


.. currentmodule:: pytrimal


.. only:: html

    Alignment
    ---------

    .. autosummary::
        :nosignatures:

        pytrimal.Alignment
        pytrimal.TrimmedAlignment
        pytrimal.AlignmentResidues
        pytrimal.AlignmentSequences


    Trimmer
    -------

    .. autosummary::
       :nosignatures:

       pytrimal.BaseTrimmer
       pytrimal.AutomaticTrimmer
       pytrimal.ManualTrimmer
       pytrimal.RepresentativeTrimmer
       pytrimal.OverlapTrimmer


    SimilarityMatrix
    ----------------

    .. autosummary::
       :nosignatures:

       pytrimal.SimilarityMatrix