Applying a time-reversible nucleotide model#

We display the available set of nucleotide substitution models.

from cogent3 import available_models

available_models("nucleotide")
Specify a model using 'Abbreviation' (case sensitive).
Model TypeAbbreviationDescription
nucleotideBHBarry and Hartigan Discrete Time substitution model Barry and Hartigan 1987. Biometrics 43: 261–76.
nucleotideDTDiscrete Time substitution model (non-stationary, non-reversible). motif_length=2 makes this a dinucleotide model, motif_length=3 a trinucleotide model.
nucleotideGNGeneral Markov Nucleotide (non-stationary, non-reversible). Kaehler, Yap, Zhang, Huttley, 2015, Sys Biol 64 (2): 281–93
nucleotidessGNstrand-symmetric general Markov nucleotide (non-stationary, non-reversible). Kaehler, 2017, Journal of Theoretical Biology 420: 144–51
nucleotideK80Kimura 1980
nucleotideJC69Jukes and Cantor's 1969 model
nucleotideGTRGeneral Time Reversible nucleotide substitution model.
nucleotideTN93Tamura and Nei 1993 model
nucleotideHKY85Hasegawa, Kishino and Yano 1985 model
nucleotideF81Felsenstein's 1981 model

10 rows x 3 columns

Using the GTR model#

We specify the general time-reversible model (Lanave et al) by its abbreviation. By default, this model does not optimise the codon frequencies but uses the average estimated from the alignment. We configure the model to optimise the root motif probabilities.

from cogent3 import get_app

loader = get_app("load_aligned", format="fasta", moltype="dna")
aln = loader("data/primate_brca1.fasta")
model = get_app("model",
    "GTR", tree="data/primate_brca1.tree", optimise_motif_probs=True
)
result = model(aln)
result
GTR
keylnLnfpDLCunique_Q
'GTR'-6992.576919TrueTrue
result.lf

GTR

log-likelihood = -6992.5769

number of free parameters = 19

Global params
A/CA/GA/TC/GC/T
1.22965.24780.94732.33895.9666
Edge params
edgeparentlength
Galagoroot0.1727
HowlerMonroot0.0448
Rhesusedge.30.0215
Orangutanedge.20.0077
Gorillaedge.10.0025
Humanedge.00.0060
Chimpanzeeedge.00.0028
edge.0edge.10.0000
edge.1edge.20.0034
edge.2edge.30.0119
edge.3root0.0076
Motif params
ACGT
0.37920.17190.20660.2423