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.. jupyter-execute::
:hide-code:
import set_working_directory
Using a protein model
=====================
We use apps to load unaligned DNA sequences and to translate them into amino acids.
.. jupyter-execute::
:raises:
from cogent3 import get_app
loader = get_app("load_unaligned", format="fasta")
to_aa = get_app("translate_seqs")
process = loader + to_aa
seqs = process("data/SCA1-cds.fasta")
Protein alignment with default settings
---------------------------------------
The default setting for "protein" is a WG01 model.
.. jupyter-execute::
:raises:
from cogent3 import get_app
aa_aligner = get_app("progressive_align", "protein")
aligned = aa_aligner(seqs)
aligned
Specify a different distance measure for estimating the guide tree
------------------------------------------------------------------
The distance measures available are percent or paralinear.
.. note:: An estimated guide tree has its branch lengths scaled so they are consistent with usage in a codon model.
.. jupyter-execute::
:raises:
aa_aligner = get_app("progressive_align", "protein", distance="paralinear")
aligned = aa_aligner(seqs)
aligned
Alignment settings and file provenance are recorded in the ``info`` attribute
-----------------------------------------------------------------------------
.. jupyter-execute::
:raises:
aligned.info
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