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.. jupyter-execute::
:hide-code:
import set_working_directory
Using a nucleotide model
------------------------
We load the unaligned sequences we will use in our examples.
.. jupyter-execute::
from cogent3 import get_app
loader = get_app("load_unaligned", format="fasta")
seqs = loader("data/SCA1-cds.fasta")
.. note:: We use an app loader, but since this is just a single file we could have used the ``cogent3.load_unaligned_seqs()`` function.
Nucleotide alignment with default settings
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The default setting for "nucleotide" is a HKY85 model.
.. jupyter-execute::
from cogent3 import get_app
nt_aligner = get_app("progressive_align", "nucleotide")
aligned = nt_aligner(seqs)
aligned
.. note:: If you specify ``unique_guides=True``, a guide tree will be estimated for every alignment.
Specify a different distance measure for estimating the guide tree
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
For the nucleotide case, you can use TN93 or paralinear.
.. jupyter-execute::
nt_aligner = get_app("progressive_align", "nucleotide", distance="TN93")
aligned = nt_aligner(seqs)
aligned
Providing a guide tree
^^^^^^^^^^^^^^^^^^^^^^
.. jupyter-execute::
tree = "((Chimp:0.001,Human:0.001):0.0076,Macaque:0.01,((Rat:0.01,Mouse:0.01):0.02,Mouse_Lemur:0.02):0.01)"
nt_aligner = get_app("progressive_align", "nucleotide", guide_tree=tree)
aligned = nt_aligner(seqs)
aligned
.. warning:: The guide tree must have branch lengths, otherwise a ``ValueError`` is raised.
Specifying the substitution model
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
You can use any ``cogent3`` nucleotide substitution model. For a list of all available, see ``cogent3.available_models()``.
.. jupyter-execute::
tree = "((Chimp:0.001,Human:0.001):0.0076,Macaque:0.01,((Rat:0.01,Mouse:0.01):0.02,Mouse_Lemur:0.02):0.01)"
nt_aligner = get_app("progressive_align", "F81", guide_tree=tree)
aligned = nt_aligner(seqs)
aligned
Alignment settings and file provenance are recorded in the ``info`` attribute
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. jupyter-execute::
aligned.info
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