Covarion.Huelsenbeck02 — The Huelsenbeck Covarion Model
Usage
Covarion.Huelsenbeck02(submodel: DiscreteDist<CTMC<a>>,
r: Double, pi1: Double) → DiscreteDist<CTMC<a>>
Arguments
A default beginning with ~ specifies a prior
distribution.
-
submodel: -
The base model
-
r: -
s01 + s10
-
Default:
~Gamma(2,1/4) -
pi1: -
Fraction of time spent in the ON state
-
Default:
~Beta(2,2)
Description
The Huelsenbeck covarion model adds among-site rate heterogeneity to the Tuffley-Steel covarion model. However, instead of scaling the Tuffley-Steel covarion rate matrix by factor F[i] for bin i, the Huelsenbeck approach involves scaling the Q matrix for bin i by F[i] before constructing the Tuffley-Steel rate matrix. This has the benefit that sites with faster evolution do not switch between ON and OFF at a faster rate.
Examples
GTR +> ASRV.Gamma +> Covarion.Huelsenbeck02GTR +> ASRV.Free +> Covarion.Huelsenbeck02Citation
Huelsenbeck, John P (2002). Testing a covariotide model of DNA substitution. Molecular Biology and Evolution 19(5): 698--707. DOI: 10.1093/oxfordjournals.molbev.a004128