paml.codeml: Estimate parameters from the M3 codon substitution model
In synDss: Recombination detection using synonymous distances

Description Usage Arguments Value Author(s) References

This function takes a sequence alignment dataset and an assumed tree, and infers the M3 model parameters kappa, p and omega (p and omega are vectors). Internal function, used within parametric bootstrap.

1	paml.codeml(data, tree, call="codeml")

`data`	Sequence alignment dataset, an object of class `"alignment"`
`tree`	Phylogenetic tree as an object of class `"phylo"`
`call`	Command to the codeml executable

Vector of kappa, p and omega

Peter Chi pchi@calpoly.edu

Z. Yang and R. Nielsen. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Molecular Biology and Evolution, 19:908-917, 2002.

synDss documentation built on May 2, 2019, 5:40 p.m.