Chapter XXX Codon Alignment
===========================

This chapter is about Codon Alignments, which is a special case of
nucleotide alignment in which the trinucleotides correspond directly to
amino acids in the translated protein product. Codon Alignment carries
information that can be used for many evolutionary analysis.

This chapter has been divided into four parts to explain the codon
alignment support in Biopython. First, a general introduction about the
basic classes in ``Bio.codonalign`` will be given. Then, a typical
procedure of how to obtain a codon alignment within Biopython is then
discussed. Next, some simple applications of codon alignment, such as
dN/dS ratio estimation and neutrality test and so forth will be covered.
Finally, IO support of codon alignment will help user to conduct
analysis that cannot be done within Biopython.

X.1 ``CodonSeq`` Class
----------------------

``Bio.codonalign.CodonSeq`` object is the base object in Codon
Alignment. It is similar to ``Bio.Seq`` but with some extra attributes.
To obtain a simple ``CodonSeq`` object, you just need to give a ``str``
object of nucleotide sequence whose length is a multiple of 3 (This can
be violated if you have ``rf_table`` argument). For example:

.. code:: pycon

   >>> from Bio.codonalign import CodonSeq
   >>> codon_seq = CodonSeq("AAATTTCCCGGG")
   >>> codon_seq
   CodonSeq('AAATTTCCCGGG')

An error will raise up if the input sequence is not a multiple of 3.

.. code:: pycon

   >>> codon_seq = CodonSeq("AAATTTCCCGG")
   Traceback (most recent call last):
   ...
   ValueError: Sequence length is not a multiple of three (i.e. a whole number of codons)

The slice of ``CodonSeq`` is exactly the same with ``Seq`` and it will
always return a ``Seq`` object if you sliced a ``CodonSeq``. For
example:

.. code:: pycon

   >>> codon_seq1 = CodonSeq("AAA---CCCGGG")
   >>> codon_seq1
   CodonSeq('AAA---CCCGGG')
   >>> codon_seq1[:6]
   Seq('AAA---')
   >>> codon_seq1[1:5]
   Seq('AA--')

``CodonSeq`` objects have a ``rf_table`` attribute that dictates how the
``CodonSeq`` will be translated by indicating the starting position of
each codon in the sequence). This is useful if your sequence is known to
have frameshift events or pseudogene that has insertion or deletion. You
might notice that in the previous example, you haven’t specify the
``rf_table`` when initiate a ``CodonSeq`` object. In fact, ``CodonSeq``
object will automatically assign a ``rf_table`` to the ``CodonSeq`` if
you don’t say anything about it.

.. code:: pycon

   >>> codon_seq1 = CodonSeq("AAACCCGGG")
   >>> codon_seq1
   CodonSeq('AAACCCGGG')
   >>> codon_seq1.rf_table
   [0, 3, 6]
   >>> codon_seq1.translate()
   'KPG'
   >>> codon_seq2 = CodonSeq("AAACCCGG", rf_table=[0, 3, 5])
   >>> codon_seq2.rf_table
   [0, 3, 5]
   >>> codon_seq2.translate()
   'KPR'

In the example, we didn’t assign ``rf_table`` to ``codon_seq1``. By
default, ``CodonSeq`` will automatically generate a ``rf_table`` to the
coding sequence assuming no frameshift events. In this case, it is
``[0, 3, 6]``, which means the first codon in the sequence starts at
position 0, the second codon in the sequence starts at position 3, and
the third codon in the sequence starts at position 6. In ``codon_seq2``,
we only have 8 nucleotides in the sequence, but with ``rf_table`` option
specified. In this case, the third codon starts at the 5th position of
the sequence rather than the 6th. And the ``translate()`` function will
use the ``rf_table`` to get the translated amino acid sequence.

Another thing to keep in mind is that ``rf_table`` will only be applied
to ungapped nucleotide sequence. This makes ``rf_table`` to be
interchangeable between ``CodonSeq`` with the same sequence but
different gaps inserted. For example,

.. code:: pycon

   >>> codon_seq1 = CodonSeq("AAACCC---GGG")
   >>> codon_seq1.rf_table
   [0, 3, 6]
   >>> codon_seq1.translate()
   'KPG'
   >>> codon_seq1.full_translate()
   'KP-G'

We can see that the ``rf_table`` of ``codon_seq1`` is still
``[0, 3, 6]``, even though we have gaps added. The ``translate()``
function will skip the gaps and return the ungapped amino acid sequence.
If gapped protein sequence is what you need, ``full_translate()`` comes
to help.

It is also easy to convert ``Seq`` object to ``CodonSeq`` object, but it
is the user’s responsibility to ensure all the necessary information is
correct for a ``CodonSeq`` (mainly ``rf_table``).

.. code:: pycon

   >>> from Bio.Seq import Seq
   >>> codon_seq = CodonSeq()
   >>> seq = Seq('AAAAAA')
   >>> codon_seq.from_seq(seq)
   CodonSeq('AAAAAA')
   >>> seq = Seq('AAAAA')
   >>> codon_seq.from_seq(seq)
   Traceback (most recent call last):
   ...
   ValueError: Sequence length is not a multiple of three (i.e. a whole number of codons)
   >>> codon_seq.from_seq(seq, rf_table=(0, 2))
   CodonSeq('AAAAA')

X.2 ``CodonAlignment`` Class
----------------------------

The ``CodonAlignment`` class is another new class in ``Codon.Align``.
Its aim is to store codon alignment data and apply various analysis upon
it. Similar to ``MultipleSeqAlignment``, you can use numpy style slice
to a ``CodonAlignment``. However, once you sliced, the returned result
will always be a ``MultipleSeqAlignment`` object.

.. code:: pycon

   >>> from Bio.codonalign import CodonSeq, CodonAlignment
   >>> from Bio.SeqRecord import SeqRecord
   >>> a = SeqRecord(CodonSeq("AAAACGTCG"), id="Alpha")
   >>> b = SeqRecord(CodonSeq("AAA---TCG"), id="Beta")
   >>> c = SeqRecord(CodonSeq("AAAAGGTGG"), id="Gamma")
   >>> codon_aln = CodonAlignment([a, b, c])
   >>> print(codon_aln)
   CodonAlignment with 3 rows and 9 columns (3 codons)
   AAAACGTCG Alpha
   AAA---TCG Beta
   AAAAGGTGG Gamma
   >>> codon_aln[0]
   SeqRecord(seq=CodonSeq('AAAACGTCG'), id='Alpha', name='<unknown name>', description='<unknown description>', dbxrefs=[])
   >>> print(codon_aln[:, 3])
   A-A
   >>> print(codon_aln[1:, 3:10])
   Alignment with 2 rows and 6 columns
   ---TCG Beta
   AGGTGG Gamma

You can write out ``CodonAlignment`` object just as what you do with
``MultipleSeqAlignment``.

.. code:: pycon

   >>> from Bio import AlignIO
   >>> AlignIO.write(codon_aln, 'example.aln', 'clustal')
   1

An alignment file called ``example.aln`` can then be found in your
current working directory. You can write ``CodonAlignment`` out in any
MSA format that Biopython supports.

Currently, you are not able to read MSA data as a ``CodonAlignment``
object directly (because of dealing with ``rf_table`` issue for each
sequence). However, you can read the alignment data in as a
``MultipleSeqAlignment`` object and convert them into ``CodonAlignment``
object using ``from_msa()`` class method. For example,

.. code:: pycon

   >>> aln = AlignIO.read('example.aln', 'clustal')
   >>> codon_aln = CodonAlignment()
   >>> print(codon_aln.from_msa(aln))
   CodonAlignment with 3 rows and 9 columns (3 codons)
   AAAACGTCG Alpha
   AAA---TCG Beta
   AAAAGGTGG Gamma

Note, the ``from_msa()`` method assume there is no frameshift events
occurs in your alignment. Its behavior is not guaranteed if your
sequence contains frameshift events!!

There is a couple of methods that can be applied to ``CodonAlignment``
class for evolutionary analysis. We will cover them more in X.4.

X.3 Build a Codon Alignment
---------------------------

Building a codon alignment is the first step of many evolutionary
anaysis. But how to do that? ``Bio.codonalign`` provides you an easy
function ``build()`` to achieve all. The data you need to prepare in
advance is a protein alignment and a set of DNA sequences that can be
translated into the protein sequences in the alignment.

``codonalign.build`` method requires two mandatory arguments. The first
one should be a protein ``MultipleSeqAlignment`` object and the second
one is a list of nucleotide ``SeqRecord`` object. By default,
``codonalign.build`` assumes the order of the alignment and nucleotide
sequences are in the same. For example:

.. code:: pycon

   >>> from Bio import codonalign
   >>> from Bio.Align import MultipleSeqAlignment
   >>> from Bio.SeqRecord import SeqRecord
   >>> from Bio.Seq import Seq
   >>> nucl1 = SeqRecord(Seq('AAATTTCCCGGG'), id='nucl1')
   >>> nucl2 = SeqRecord(Seq('AAATTACCCGCG'), id='nucl2')
   >>> nucl3 = SeqRecord(Seq('ATATTACCCGGG'), id='nucl3')
   >>> prot1 = SeqRecord(nucl1.seq.translate(), id='prot1')
   >>> prot2 = SeqRecord(nucl2.seq.translate(), id='prot2')
   >>> prot3 = SeqRecord(nucl3.seq.translate(), id='prot3')
   >>> aln = MultipleSeqAlignment([prot1, prot2, prot3])
   >>> codon_aln = codonalign.build(aln, [nucl1, nucl2, nucl3])
   >>> print(codon_aln)
   CodonAlignment with 3 rows and 12 columns (4 codons)
   AAATTTCCCGGG nucl1
   AAATTACCCGCG nucl2
   ATATTACCCGGG nucl3

In the above example, ``codonalign.build`` will try to match ``nucl1``
with ``prot1``, ``nucl2`` with ``prot2`` and ``nucl3`` with ``prot3``,
i.e., assuming the order of records in ``aln`` and
``[nucl1, nucl2, nucl3]`` is the same.

``codonalign.build`` method is also able to handle key match. In this
case, records with same id are paired. For example:

.. code:: pycon

   >>> nucl1 = SeqRecord(Seq('AAATTTCCCGGG'), id='nucl1')
   >>> nucl2 = SeqRecord(Seq('AAATTACCCGCG'), id='nucl2')
   >>> nucl3 = SeqRecord(Seq('ATATTACCCGGG'), id='nucl3')
   >>> prot1 = SeqRecord(nucl1.seq.translate(), id='prot1')
   >>> prot2 = SeqRecord(nucl2.seq.translate(), id='prot2')
   >>> prot3 = SeqRecord(nucl3.seq.translate(), id='prot3')
   >>> aln = MultipleSeqAlignment([prot1, prot2, prot3])
   >>> nucl = {'prot1': nucl1, 'prot2': nucl2, 'prot3': nucl3}
   >>> codon_aln = codonalign.build(aln, nucl)
   >>> print(codon_aln)
   CodonAlignment with 3 rows and 12 columns (4 codons)
   AAATTTCCCGGG nucl1
   AAATTACCCGCG nucl2
   ATATTACCCGGG nucl3

This option is useful if you read nucleotide sequences using
``SeqIO.index`` method, in which case the nucleotide dict with be
generated automatically.

Sometimes, you are neither not able to ensure the same order or the same
id. ``codonalign.build`` method provides you an manual approach to tell
the program nucleotide sequence and protein sequence correspondance by
generating a ``corr_dict``. ``corr_dict`` should be a dictionary that
uses protein record id as key and nucleotide record id as item. Let’s
look at an example:

.. code:: pycon

   >>> nucl1 = SeqRecord(Seq('AAATTTCCCGGG'), id='nucl1')
   >>> nucl2 = SeqRecord(Seq('AAATTACCCGCG'), id='nucl2')
   >>> nucl3 = SeqRecord(Seq('ATATTACCCGGG'), id='nucl3')
   >>> prot1 = SeqRecord(nucl1.seq.translate(), id='prot1')
   >>> prot2 = SeqRecord(nucl2.seq.translate(), id='prot2')
   >>> prot3 = SeqRecord(nucl3.seq.translate(), id='prot3')
   >>> aln = MultipleSeqAlignment([prot1, prot2, prot3])
   >>> corr_dict = {'prot1': 'nucl1', 'prot2': 'nucl2', 'prot3': 'nucl3'}
   >>> codon_aln = codonalign.build(aln, [nucl3, nucl1, nucl2], corr_dict=corr_dict)
   >>> print(codon_aln)
   CodonAlignment with 3 rows and 12 columns (4 codons)
   AAATTTCCCGGG nucl1
   AAATTACCCGCG nucl2
   ATATTACCCGGG nucl3

We can see, even though the second argument of ``codonalign.build`` is
not in the same order with ``aln`` in the above example, the
``corr_dict`` tells the program to pair protein records and nucleotide
records. And we are still able to obtain the correct ``codonalignment``
object.

The underlying algorithm of ``codonalign.build`` method is very similar
to ``pal2nal`` (a very famous perl script to build codon alignment).
``codonalign.build`` will first translate protein sequences into a long
degenerate regular expression and tries to find a match in its
corresponding nucleotide sequence. When translation fails, it divides
protein sequence into several small anchors and tries to match each
anchor to the nucleotide sequence to figure out where the mismatch and
frameshift events lie. Other options available for ``codonalign.build``
includes ``anchor_len`` (default 10) and ``max_score`` (maximum
tolerance of unexpected events, default 10). You may want to refer the
Biopython build-in help to get more information about these options.

Now let’s look at a real example of building codon alignment. Here we
will use epidermal growth factor (EGFR) gene to demonstrate how to
obtain codon alignment. To reduce your effort, we have already collected
EGFR sequences for Homo sapiens, Bos taurus, Rattus norvegicus, Sus
scrofa and Drosophila melanogaster. The three files used in this example
(``egfr_nucl.fa`` with the nucleotide sequences of EGFR,
``egfr_pro.aln`` with the EGFR protein sequence alignment in ``clustal``
format, and ``egfr_id`` with the id correspondance between protein
records and nucleotide records) is available from the ‘Tests/codonalign‘
directory in the Biopython distribution. You can then try the following
code (make sure the files are in your current python working directory):

.. code:: pycon

   >>> from Bio import SeqIO, AlignIO
   >>> nucl = SeqIO.parse('egfr_nucl.fa', 'fasta')
   >>> prot = AlignIO.read('egfr_pro.aln', 'clustal')
   >>> id_corr = {i.split()[0]: i.split()[1] for i in open('egfr_id').readlines()}
   >>> aln = codonalign.build(prot, nucl, corr_dict=id_corr)
   /biopython/Bio/codonalign/__init__.py:568: UserWarning: gi|47522840|ref|NP_999172.1|(L 449) does not correspond to gi|47522839|ref|NM_214007.1|(ATG)
     % (pro.id, aa, aa_num, nucl.id, this_codon))
   >>> print(aln)
   CodonAlignment with 6 rows and 4446 columns (1482 codons)
   ATGATGATTATCAGCATGTGGATGAGCATATCGCGAGGATTGTGGGACAGCAGCTCC...GTG gi|24657088|ref|NM_057410.3|
   ---------------------ATGCTGCTGCGACGGCGCAACGGCCCCTGCCCCTTC...GTG gi|24657104|ref|NM_057411.3|
   ------------------------------ATGAAAAAGCACGAG------------...GCC gi|302179500|gb|HM749883.1|
   ------------------------------ATGCGACGCTCCTGGGCGGGCGGCGCC...GCA gi|47522839|ref|NM_214007.1|
   ------------------------------ATGCGACCCTCCGGGACGGCCGGGGCA...GCA gi|41327737|ref|NM_005228.3|
   ------------------------------ATGCGACCCTCAGGGACTGCGAGAACC...GCA gi|6478867|gb|M37394.2|RATEGFR

We can see, while building the codon alignment a mismatch event is
found. And this is shown as a UserWarning.

X.4 Codon Alignment Application
-------------------------------

The most important application of codon alignment is to estimate
nonsynonymous substitutions per site (dN) and synonymous substitutions
per site (dS). ``codonalign`` currently support three counting based
methods (NG86, LWL85, YN00) and maximum likelihood method to estimate dN
and dS. The function to conduct dN, dS estimation is called
``cal_dn_ds``. When you obtained a codon alignment, it is quite easy to
calculate dN and dS. For example (assuming you have EGFR codon alignmnet
in the python working space):

.. code:: pycon

   >>> from Bio.codonalign.codonseq import cal_dn_ds
   >>> print(aln)
   CodonAlignment with 6 rows and 4446 columns (1482 codons)
   ATGATGATTATCAGCATGTGGATGAGCATATCGCGAGGATTGTGGGACAGCAGCTCC...GTG gi|24657088|ref|NM_057410.3|
   ---------------------ATGCTGCTGCGACGGCGCAACGGCCCCTGCCCCTTC...GTG gi|24657104|ref|NM_057411.3|
   ------------------------------ATGAAAAAGCACGAG------------...GCC gi|302179500|gb|HM749883.1|
   ------------------------------ATGCGACGCTCCTGGGCGGGCGGCGCC...GCA gi|47522839|ref|NM_214007.1|
   ------------------------------ATGCGACCCTCCGGGACGGCCGGGGCA...GCA gi|41327737|ref|NM_005228.3|
   ------------------------------ATGCGACCCTCAGGGACTGCGAGAACC...GCA gi|6478867|gb|M37394.2|RATEGFR
   >>> dN, dS = cal_dn_ds(aln[0], aln[1], method='NG86')
   >>> print(dN, dS)
   0.0209078305058 0.0178371876389
   >>> dN, dS = cal_dn_ds(aln[0], aln[1], method='LWL85')
   >>> print(dN, dS)
   0.0203061425453 0.0163935691992
   >>> dN, dS = cal_dn_ds(aln[0], aln[1], method='YN00')
   >>> print(dN, dS)
   0.0198195580321 0.0221560648799
   >>> dN, dS = cal_dn_ds(aln[0], aln[1], method='ML')
   >>> print(dN, dS)
   0.0193877676103 0.0217247139962

If you are using maximum likelihood methdo to estimate dN and dS, you
are also able to specify equilibrium codon frequency to ``cfreq``
argument. Available options include ``F1x4``, ``F3x4`` and ``F61``.

It is also possible to get dN and dS matrix or a tree from a
``CodonAlignment`` object.

.. code:: pycon

   >>> dn_matrix, ds_matrix = aln.get_dn_ds_matrix()
   >>> print(dn_matrix)
   gi|24657088|ref|NM_057410.3|    0
   gi|24657104|ref|NM_057411.3|    0.0209078305058 0
   gi|302179500|gb|HM749883.1|     0.611523924924  0.61022032668   0
   gi|47522839|ref|NM_214007.1|    0.614035083563  0.60401686212   0.0411803504059 0
   gi|41327737|ref|NM_005228.3|    0.61415325314   0.60182631356   0.0670105144563 0.0614703609541 0
   gi|6478867|gb|M37394.2|RATEGFR  0.61870883409   0.606868724887  0.0738690303483 0.0735789092792 0.0517984707257 0
   gi|24657088|ref|NM_057410.3|    gi|24657104|ref|NM_057411.3|    gi|302179500|gb|HM749883.1| gi|47522839|ref|NM_214007.1|    gi|41327737|ref|NM_005228.3|    gi|6478867|gb|M37394.2|RATEGFR
   >>> dn_tree, ds_tree = aln.get_dn_ds_tree()
   >>> print(dn_tree)
   Tree(rooted=True)
       Clade(branch_length=0, name='Inner5')
           Clade(branch_length=0.279185347322, name='Inner4')
               Clade(branch_length=0.00859186651689, name='Inner3')
                   Clade(branch_length=0.0258992353629, name='gi|6478867|gb|M37394.2|RATEGFR')
                   Clade(branch_length=0.0258992353629, name='gi|41327737|ref|NM_005228.3|')
               Clade(branch_length=0.0139009266768, name='Inner2')
                   Clade(branch_length=0.020590175203, name='gi|47522839|ref|NM_214007.1|')
                   Clade(branch_length=0.020590175203, name='gi|302179500|gb|HM749883.1|')
           Clade(branch_length=0.294630667432, name='Inner1')
               Clade(branch_length=0.0104539152529, name='gi|24657104|ref|NM_057411.3|')
               Clade(branch_length=0.0104539152529, name='gi|24657088|ref|NM_057410.3|')

Another application of codon alignment that ``codonalign`` supports is
Mcdonald-Kreitman test. This test compares the within species synonymous
substitutions and nonsynonymous substitutions and between species
synonymous substitutions and nonsynonymous substitutions to see if they
are from the same evolutionary process. The test requires gene sequences
sampled from different individuals of the same species. In the following
example, we will use Adh gene from fluit fly to demonstrate how to
conduct the test. The data includes 11 individuals from D. melanogaster,
4 individuals from D. simulans and 12 individuals from D. yakuba. The
data is available in the ‘Tests/codonalign‘ directory in the Biopython
distribution. A function called ``mktest`` will be used for the test.

.. code:: pycon

   >>> from Bio import SeqIO, AlignIO
   >>> from Bio.codonalign import build
   >>> from Bio.codonalign.codonalignment import mktest
   >>> pro_aln = AlignIO.read('adh.aln', 'clustal')
   >>> p = SeqIO.index('drosophilla.fasta', 'fasta')
   >>> codon_aln = build(pro_aln, p)
   >>> print(codon_aln)
   CodonAlignment with 27 rows and 768 columns (256 codons)
   ATGGCGTTTACCTTGACCAACAAGAACGTGGTTTTCGTGGCCGGTCTGGGAGGCATT...ATC gi|9217|emb|X57365.1|
   ATGGCGTTTACCTTGACCAACAAGAACGTGGTTTTCGTGGCCGGTCTGGGAGGCATT...ATC gi|9219|emb|X57366.1|
   ATGGCGTTTACCTTGACCAACAAGAACGTGGTTTTCGTGGCCGGTCTGGGAGGCATT...ATC gi|9221|emb|X57367.1|
   ATGGCGTTTACCTTGACCAACAAGAACGTGGTTTTCGTGGCCGGTCTGGGAGGCATT...ATC gi|9223|emb|X57368.1|
   ATGGCGTTTACCTTGACCAACAAGAACGTGGTTTTCGTGGCCGGTCTGGGAGGCATT...ATC gi|9225|emb|X57369.1|
   ATGGCGTTTACCTTGACCAACAAGAACGTGGTTTTCGTGGCCGGTCTGGGAGGCATT...ATC gi|9227|emb|X57370.1|
   ATGGCGTTTACCTTGACCAACAAGAACGTGGTTTTCGTGGCCGGTCTGGGAGGCATT...ATC gi|9229|emb|X57371.1|
   ATGGCGTTTACCTTGACCAACAAGAACGTGGTTTTCGTGGCCGGTCTGGGAGGCATT...ATC gi|9231|emb|X57372.1|
   ATGGCGTTTACCTTGACCAACAAGAACGTGGTTTTCGTGGCCGGTCTGGGAGGCATT...ATC gi|9233|emb|X57373.1|
   ATGGCGTTTACCTTGACCAACAAGAACGTGGTTTTCGTGGCCGGTCTGGGAGGCATT...ATC gi|9235|emb|X57374.1|
   ATGGCGTTTACCTTGACCAACAAGAACGTGGTTTTCGTGGCCGGTCTGGGAGGCATT...ATC gi|9237|emb|X57375.1|
   ATGGCGTTTACCTTGACCAACAAGAACGTGGTTTTCGTGGCCGGTCTGGGAGGCATT...ATC gi|9239|emb|X57376.1|
   ATGGCGTTTACTTTGACCAACAAGAACGTGATTTTCGTTGCCGGTCTGGGAGGCATT...ATC gi|9097|emb|X57361.1|
   ATGGCGTTTACTTTGACCAACAAGAACGTGATTTTCGTTGCCGGTCTGGGAGGCATT...ATC gi|9099|emb|X57362.1|
   ATGGCGTTTACTTTGACCAACAAGAACGTGATTTTCGTTGCCGGTCTGGGAGGCATT...ATC gi|9101|emb|X57363.1|
   ATGGCGTTTACTTTGACCAACAAGAACGTGATTTTCGTTGCCGGTCTGGGAGGCATC...ATC gi|9103|emb|X57364.1|
   ATGTCGTTTACTTTGACCAACAAGAACGTGATTTTCGTGGCCGGTCTGGGAGGCATT...ATC gi|156879|gb|M17837.1|DROADHCK
   ATGTCGTTTACTTTGACCAACAAGAACGTGATTTTCGTGGCCGGTCTGGGAGGCATT...ATC gi|156877|gb|M17836.1|DROADHCJ
   ATGTCGTTTACTTTGACCAACAAGAACGTGATTTTCGTGGCCGGTCTGGGAGGCATT...ATC gi|156875|gb|M17835.1|DROADHCI
   ATGTCGTTTACTTTGACCAACAAGAACGTGATTTTCGTGGCCGGTCTGGGAGGCATT...ATC gi|156873|gb|M17834.1|DROADHCH
   ATGTCGTTTACTTTGACCAACAAGAACGTGATTTTCGTGGCCGGTCTGGGAGGCATT...ATC gi|156871|gb|M17833.1|DROADHCG
   ATGTCGTTTACTTTGACCAACAAGAACGTGATTTTCGTTGCCGGTCTGGGAGGCATT...ATC gi|156863|gb|M19547.1|DROADHCC
   ATGTCGTTTACTTTGACCAACAAGAACGTGATTTTCGTGGCCGGTCTGGGAGGCATT...ATC gi|156869|gb|M17832.1|DROADHCF
   ATGTCGTTTACTTTGACCAACAAGAACGTGATTTTCGTGGCCGGTCTGGGAGGCATT...ATC gi|156867|gb|M17831.1|DROADHCE
   ATGTCGTTTACTTTGACCAACAAGAACGTGATTTTCGTTGCCGGTCTGGGAGGCATT...ATC gi|156865|gb|M17830.1|DROADHCD
   ATGTCGTTTACTTTGACCAACAAGAACGTGATTTTCGTTGCCGGTCTGGGAGGCATT...ATC gi|156861|gb|M17828.1|DROADHCB
   ATGTCGTTTACTTTGACCAACAAGAACGTGATTTTCGTTGCCGGTCTGGGAGGCATT...ATC gi|156859|gb|M17827.1|DROADHCA

   >>> print(mktest([codon_aln[1:12], codon_aln[12:16], codon_aln[16:]]))
   0.00206457257254

In the above example, ``codon_aln[1:12]`` belongs to D. melanogaster,
``codon_aln[12:16]`` belongs to D. simulans and ``codon_aln[16:]``
belongs to D. yakuba. ``mktest`` will return the p-value of the test. We
can see in this case, 0.00206 << 0.01, therefore, the gene is under
strong negative selection according to MK test.

X.4 Future Development
----------------------

Because of the limited time frame for Google Summer of Code project,
some of the functions in ``codonalign`` is not tested comprehensively.
In the following days, I will continue perfect the code and several new
features will be added. I am always welcome to hear your suggestions and
feature request. You are also highly encouraged to contribute to the
existing code. Please do not hesitable to email me (zruan1991 at gmail
dot com) when you have novel ideas that can make the code better.
