LG
Usage
LG(a: AA)
→ 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 LG08 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(LG_freq).
Examples
LGLG +> FLG +> F(LG_freq)Citation
Le, Si Quang; Gascuel, Olivier (2008). An Improved General Amino Acid Replacement Matrix. Molecular Biology and Evolution 25(7): 1307--1320. DOI: 10.1093/molbev/msn067