`WAG`

Usage

WAG(a: a)
→ ExchangeModel<AA>

Arguments

a:: The alphabet; Default: The alphabet in the current context

Original default expressions

a

get_state(alphabet)

Description

Empirically derived exchangability matrix for general proteins.

This command only refers to the symmetric part of the WAG model, not the frequencies. Frequencies are added by using the +> F command. Frequencies are estimated by default but can be fixed to the values estimated in the paper using +> F(WAG_freq).

Examples

WAG

WAG +> F

WAG +> F(WAG_freq)

Citation

Whelan, Simon; Goldman, Nick (2001). A General Empirical Model of Protein Evolution Derived from Multiple Protein Families Using a Maximum-Likelihood Approach. Molecular Biology and Evolution 18(5): 691--699. DOI: 10.1093/oxfordjournals.molbev.a003851