`ASRV.Gamma` — The Gamma rate heterogeneity model

Usage

ASRV.Gamma(submodel: DiscreteDist<CTMC<a>>,
n: Int, alpha: Double) → DiscreteDist<CTMC<a>>

Aliases: G

Arguments

A default beginning with ~ specifies a prior distribution.

submodel:: The model being scaled
n:: The number of equal-probability Gamma categories; Default: 4
alpha:: The shape parameter for the Gamma distribution; Default: ~LogLaplace(6,2)

Description

This model divides a unit-mean Gamma distribution into equal-probability categories and represents each category by its conditional mean.

Examples

GTR +> ASRV.Gamma(4) +> Inv

Citation

Yang, Ziheng (1994). Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. Journal of molecular evolution 39(3): 306--314. DOI: 10.1007/BF00160154