Using a codon model#

We load the unaligned sequences we will use in our examples.

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.

Codon alignment with default settings#

The default settings will result in estimation of a guide tree (using percent identity between the sequences). The default “codon” model is MG94HKY.

from cogent3 import get_app

codon_aligner = get_app("progressive_align", "codon")
aligned = codon_aligner(seqs)
aligned
0
HumanATGAAATCCAACCAAGAGCGGAGCAACGAATGCCTGCCTCCCAAGAAGCGCGAGATCCCC
Chimp............................................................
Macaque............................................................
Mouse Lemur..................................................T.........
Rat........T.................T....................A..T.........
Mouse...............................................A..T.........

6 x 2478 (truncated to 6 x 60) dna alignment

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#

The distance measures available are the same as for the nucleotide case (percent, TN93 or paralinear).

Note

An estimated guide tree has its branch lengths scaled so they are consistent with usage in a codon model.

nt_aligner = get_app("progressive_align", "codon", distance="paralinear")
aligned = nt_aligner(seqs)
aligned
0
HumanATGAAATCCAACCAAGAGCGGAGCAACGAATGCCTGCCTCCCAAGAAGCGCGAGATCCCC
Chimp............................................................
Macaque............................................................
Mouse Lemur..................................................T.........
Rat........T.................T....................A..T.........
Mouse...............................................A..T.........

6 x 2478 (truncated to 6 x 60) dna alignment

Providing a guide tree#

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)"
codon_aligner = get_app("progressive_align", "codon", guide_tree=tree)
aligned = codon_aligner(seqs)
aligned
0
HumanATGAAATCCAACCAAGAGCGGAGCAACGAATGCCTGCCTCCCAAGAAGCGCGAGATCCCC
Chimp............................................................
Macaque............................................................
Rat........T.................T....................A..T.........
Mouse...............................................A..T.........
Mouse Lemur..................................................T.........

6 x 2478 (truncated to 6 x 60) dna alignment

Warning

The guide tree must have branch lengths, otherwise a ValueError is raised.

Specifying the gap parameters#

codon_aligner = get_app("progressive_align",
    "codon", guide_tree=tree, indel_rate=0.001, indel_length=0.01
)
aligned = codon_aligner(seqs)
aligned
0
HumanATGAAATCCAACCAAGAGCGGAGCAACGAATGCCTGCCTCCCAAGAAGCGCGAGATCCCC
Chimp............................................................
Macaque............................................................
Rat........T.................T....................A..T.........
Mouse...............................................A..T.........
Mouse Lemur..................................................T.........

6 x 2478 (truncated to 6 x 60) dna alignment

Specifying the substitution model and parameters#

Any cogent3 codon substitution model can be used. (See cogent3.available_models().)

codon_aligner = get_app("progressive_align",
    "CNFHKY", guide_tree=tree, param_vals=dict(omega=0.1, kappa=3)
)
aligned = codon_aligner(seqs)
aligned
0
HumanATGAAATCCAACCAAGAGCGGAGCAACGAATGCCTGCCTCCCAAGAAGCGCGAGATCCCC
Chimp............................................................
Macaque............................................................
Rat........T.................T....................A..T.........
Mouse...............................................A..T.........
Mouse Lemur..................................................T.........

6 x 2478 (truncated to 6 x 60) dna alignment

Note

If you provide parameter values, those must be consistent with the model definition.

Alignment settings and file provenance are recorded in the info attribute#

The parameters used to construct the alignment, including the guide tree and substitution model, are record in the alignment info attribute.

aligned.info
{'Refs': {},
 'source': 'data/SCA1-cds.fasta',
 'align_params': {'omega': 0.1,
  'kappa': 3,
  'indel_length': 0.1,
  'indel_rate': 1e-10,
  'guide_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)'AUTOGENERATED_NAME_ZK':1e-06);",
  'model': 'CNFHKY',
  'lnL': -6211.755293809508}}