biotite.sequence.align
======================
.. currentmodule:: biotite.sequence.align

.. automodule:: biotite.sequence.align

.. currentmodule:: biotite.sequence.align


Substitution matrices
---------------------

.. autosummary::
   :nosignatures:
   :toctree:

   SubstitutionMatrix

Aligners
--------

.. autosummary::
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   :toctree:

   align_ungapped
   align_optimal
   align_local_ungapped
   align_local_gapped
   align_banded
   align_multiple

Alignments
----------

.. autosummary::
   :nosignatures:
   :toctree:

   Alignment
   get_codes
   get_symbols
   get_sequence_identity
   get_pairwise_sequence_identity
   score

k-mers
------

.. autosummary::
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   :toctree:

   KmerAlphabet
   KmerTable
   BucketKmerTable
   SimilarityRule
   ScoreThresholdRule
   bucket_number

k-mer subset selections
-----------------------

.. autosummary::
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   :toctree:

   MinimizerSelector
   SyncmerSelector
   CachedSyncmerSelector
   MincodeSelector

k-mer permutations
------------------

.. autosummary::
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   :toctree:

   Permutation
   RandomPermutation
   FrequencyPermutation

CIGAR strings
-------------

.. autosummary::
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   :toctree:

   CigarOp
   read_alignment_from_cigar
   write_alignment_to_cigar

Miscellaneous
-------------

.. autosummary::
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   :toctree:

   EValueEstimator
   find_terminal_gaps
   remove_terminal_gaps