# Bio.codonalign.codonalignment module

Code for dealing with Codon Alignment.

CodonAlignment class is inherited from MultipleSeqAlignment class. This is the core class to deal with codon alignment in biopython.

class Bio.codonalign.codonalignment.CodonAlignment(records='', name=None)

  Bases: `MultipleSeqAlignment`

  Codon Alignment class that inherits from MultipleSeqAlignment.

      >>> from Bio.SeqRecord import SeqRecord
      >>> a = SeqRecord(CodonSeq("AAAACGTCG"), id="Alpha")
      >>> b = SeqRecord(CodonSeq("AAA---TCG"), id="Beta")
      >>> c = SeqRecord(CodonSeq("AAAAGGTGG"), id="Gamma")
      >>> print(CodonAlignment([a, b, c]))
      CodonAlignment with 3 rows and 9 columns (3 codons)
      AAAACGTCG Alpha
      AAA---TCG Beta
      AAAAGGTGG Gamma

  __init__(records='', name=None)

    Initialize the class.

  __str__()

    Return a multi-line string summary of the alignment.

    This output is indicated to be readable, but large alignment is shown truncated. A maximum of 20 rows (sequences) and 60 columns (20 codons) are shown, with the record identifiers. This should fit nicely on a single screen. e.g.

  __getitem__(index)

    Return a CodonAlignment object for single indexing.

  __add__(other)

    Combine two codonalignments with the same number of rows by adding them.

    The method also allows to combine a CodonAlignment object with a MultipleSeqAlignment object. The following rules apply:

    > - CodonAlignment + CodonAlignment -> CodonAlignment

    > - CodonAlignment + MultipleSeqAlignment -> MultipleSeqAlignment

  get_aln_length()

    Get alignment length.

  toMultipleSeqAlignment()

    Convert the CodonAlignment to a MultipleSeqAlignment.

    Return a MultipleSeqAlignment containing all the SeqRecord in the CodonAlignment using Seq to store sequences

  get_dn_ds_matrix(method='NG86', codon_table=None)

    Available methods include NG86, LWL85, YN00 and ML.

    Argument:

      - method - Available methods include NG86, LWL85, YN00 and ML.

      - codon_table - Codon table to use for forward translation.

  get_dn_ds_tree(dn_ds_method='NG86', tree_method='UPGMA', codon_table=None)

    Construct dn tree and ds tree.

    Argument:

      - dn_ds_method - Available methods include NG86, LWL85, YN00 and ML.

      - tree_method - Available methods include UPGMA and NJ.

  classmethod from_msa(align)

    Convert a MultipleSeqAlignment to CodonAlignment.

    Function to convert a MultipleSeqAlignment to CodonAlignment. It is the user’s responsibility to ensure all the requirement needed by CodonAlignment is met.

  __annotate_func__ = None
  __annotations_cache__ = {}
  __firstlineno__ = 26
  __static_attributes__ = ()

Bio.codonalign.codonalignment.mktest(codon_alns, codon_table=None, alpha=0.05)

  McDonald-Kreitman test for neutrality.

  Implement the McDonald-Kreitman test for neutrality (PMID: 1904993) This method counts changes rather than sites (http://mkt.uab.es/mkt/help_mkt.asp).

  Arguments:

    - codon_alns - list of CodonAlignment to compare (each CodonAlignment object corresponds to gene sampled from a species)

  Return the p-value of test result.

Biopython v: 1.86

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