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Kappa1 - relative AC, AT, TG and GC rates (float) Mygtr = GTR.standard(model='TN93', mu=, kappa1=, kappa2=) The frequencies of the nucleotides are allowed Transition: (A G) is allowed to have a different rate to (CT). The model distinguishes between the two different types of Mygtr = GTR.standard(model='T92', mu=, pi_GC=, kappa=) Extending Kimura (1980) model for the case where a Mygtr = GTR.standard(model='HKY85', mu=, pi=, kappa=) doi:10.1007/BF02101694Ĭurrent implementation of the model does not account for the gaps Nucleotides (as in F81) + distinguishes between transition/transversion substitutions Pi - : nucleotide concentrations (numpy.array)Īlphabet' - alphabet to use. Mygtr = GTR.standard(model='F81', mu=, pi=, alphabet=) Assumes non-equal concentrations across nucleotides,īut the transition rate between all states is assumed to be equal. Kappa - ratio of transversion/transition rates (float)įelsenstein 1981 model. Mygtr = GTR.standard(model='k80', mu=, kappa=) doi:10.1007/BF01731581.Ĭurrent implementation of the model does not account for the gaps. Of the transversion/transition rates is given by kappa parameter. Assumes equal concentrations across nucleotides, butĪllows different rates between transitions and transversions. My_alph - alphabet (str: 'nuc' or 'nuc_nogap') Mygtr = GTR.standard(model='jc69', mu=, alphabet=) Of the nucleotides and equal transition rates between nucleotide states.įor more info, see: Jukes and Cantor (1969).Įvolution of Protein Molecules. **kwargs – Key word arguments to be passed to the model standard ( model, ** kwargs ) Ĭreate standard model of molecular evolution. Where msg is a string and level an integer to be compared against verbose.
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Logger ( callable) – Custom logging function that should take arguments (msg, level, warn=False), Implement ambiguous characters like ‘N’= which areĮqually likely to be any of the 4 nucleotides. Prof_map ( dict) – Dictionary linking characters in the sequence to the likelihood If a numpy array of characters is passed, a new alphabet is constructed,Īnd the default profile map is atached to it.
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In this case, the alphabet and its profile map are pulled If a string is passed, it is understood asĪn alphabet name. _init_ ( alphabet = 'nuc', prof_map = None, logger = None ) GTR ( alphabet = 'nuc', prof_map = None, logger = None ) ĭefines General-Time-Reversible model of character evolution. GTR class documentation class treetime.