Models

Codon substitution model classes.

Codon Models

M0CodonModel

class crabml.models.codon.M0CodonModel(kappa=2.0, omega=0.4, pi=None)

M0 codon substitution model (one dN/dS ratio).

The M0 model has a single omega (dN/dS) parameter for all branches and sites. The substitution rate between codons depends on: - kappa (transition/transversion ratio) - omega (non-synonymous/synonymous ratio) - codon frequencies (pi)

Parameters

kappafloat

Transition/transversion rate ratio (default 2.0)

omegafloat

dN/dS ratio (default 0.4)

pinp.ndarray, shape (61,), optional

Codon equilibrium frequencies. If None, uniform frequencies are used.

__init__(kappa=2.0, omega=0.4, pi=None)

Initialize M0 codon model.

get_Q_matrix()

Construct the rate matrix Q for the M0 model.

Return type:

ndarray

Returns

np.ndarray, shape (61, 61)

Rate matrix Q (normalized to one substitution per time unit)

Site-Class Codon Models

Additional model classes:

• M1aCodonModel - Nearly neutral model

• M2aCodonModel - Positive selection model

• M3CodonModel - Discrete omegas

• M7CodonModel - Beta distribution

• M8CodonModel - Beta + omega

• M8aCodonModel - Beta + omega=1

• M4CodonModel - Fixed omegas with variable frequencies

• M5CodonModel - Gamma distribution

• M6CodonModel - 2Gamma distribution

• M9CodonModel - Beta & Gamma

All models follow similar interfaces with model-specific parameters.