Table 1 Descriptions of the model-related acronyms
Acronym | Description |
|---|---|
DT | Indicates that a model allows simultaneous double (D) and triple (T) nucleotide changes between codons |
G0 | A GPP codon model employing a single ω parameter |
G1aX | A GPP codon model with the same discrete mixture of two ω parameters as model M1a; the total number of free parameters in the model is given by X, and varies depending on how DT and exchangeabilities are modeled |
G2aX | A GPP codon model with the same discrete mixture of three ω parameters as model M2a; the total number of free parameters in the model is given by X, and varies depending on how DT and exchangeabilities are modeled |
GPP | General-Purpose Parametric (GPP) modelling framework for codons |
GTR | General Time Reversible (GTR) model for single nucleotide changes |
GY | The codon modelling framework of Goldman and Yang [26] where the transition probability is proportional to the target codon frequency |
M0 | A codon model employing a single ω parameter as implemented in PAML [54] |
M1a | A codon model employing a constrained discrete mixture of two ω parameters [45] |
M2a | A codon model employing a constrained discrete mixture of three ω parameters [45] |
M3 | A codon model employing an unconstrained discrete mixture of k independent ω parameters [6] |
M8 | A codon model employing a discretized β distribution to model among site variability in ω [6] |
MEP | Mixed Empirical and Parametric (MEP) models combine empirical estimates of exchangeabilities with so-called mechanistic parameters of codon evolution |
MG | The codon modelling framework of Muse and Gaut [47] where the transition probability is proportional to the target nucleotide frequency |
MNR | A class of models allowing Multiple Nonsynonymous Rates (MNR) of exchangeability between codons |
PCP | Physiochemical-Constrained Parametric (PCP) models parameterize the influence of physiochemical constraints on nonsynonymous changeability |
REV | A fully reversible codon model described by a 61×61 matrix Q, where all codon exchangeabilities are independent parameters of the model. |
SNR | A class of models allowing only a Single Nonsynonymous Rates (SNR) of exchangeability between codons |