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