def JTT92(**kw):
"""Jones, Taylor and Thornton 1992 empirical protein model
Jones DT, Taylor WR, Thornton JM.
The rapid generation of mutation data matrices from protein sequences.
Comput Appl Biosci. 1992 Jun;8(3):275-82.
Matrix imported from PAML jones.dat file"""
sm = substitution_model.EmpiricalProteinMatrix(
JTT92_matrix, JTT92_freqs, name='JTT92', **kw)
return sm
def DSO78(**kw):
"""Dayhoff et al 1978 empirical protein model
Dayhoff, MO, Schwartz RM, and Orcutt, BC. 1978
A model of evolutionary change in proteins. Pp. 345-352.
Atlas of protein sequence and structure, Vol 5, Suppl. 3.
National Biomedical Research Foundation, Washington D. C
Matrix imported from PAML dayhoff.dat file"""
sm = substitution_model.EmpiricalProteinMatrix(
DSO78_matrix, DSO78_freqs, name='DSO78', **kw)
return sm
def AH96(**kw):
"""Adachi and Hasegawa 1996 empirical model for mitochondrial proteins.
Adachi J, Hasegawa M.
Model of amino acid substitution in proteins encoded by mitochondrial DNA.
J Mol Evol. 1996 Apr;42(4):459-68.
Matrix imported from PAML mtREV24.dat file"""
sm = substitution_model.EmpiricalProteinMatrix(
AH96_matrix,
AH96_freqs,
name='AH96_mtREV24',
**kw)
return sm
def WG01(**kw):
"""Whelan and Goldman 2001 empirical model for globular proteins.
Whelan S, Goldman N.
A general empirical model of protein evolution derived from multiple protein
families using a maximum-likelihood approach.
Mol Biol Evol. 2001 May;18(5):691-9.
Matrix imported from PAML wag.dat file"""
sm = substitution_model.EmpiricalProteinMatrix(
WG01_matrix,
WG01_freqs,
name='WG01',
**kw)
return sm