`ASRV.Gamma_median` — The median-discretized Gamma rate heterogeneity model

Usage

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

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 uses equal-probability categories represented by their medians to approximate Gamma-distributed rates across sites. The rates are normalized to have mean one when applied to the substitution model.

Examples

GTR +> ASRV.Gamma_median(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