CompEvol
Implement the free-rate model of rates across sites
The developers may consider incorporating the free-rate model, which relaxes the assumption of Gamma rate heterogeneity without many more parameters (https://doi.org/10.1038/nmeth.4285). One can for example use Dirichlet prior for rate proportions.
There is already an implementation in the RBS package: FreeRateModel with example XML. Operators/priors may slightly differ in the implementation from the citation though.
Validated and tested?
On 16/01/2019, at 11:58 AM, Remco Bouckaert [email protected] wrote:
There is already an implementation in the RBS package: FreeRateModel https://github.com/BEAST2-Dev/rb-beast/blob/master/src/beast/evolution/sitemodel/FreeRateModel.java with example XML https://github.com/BEAST2-Dev/rb-beast/blob/master/examples/testFreeRateModel.xml. Operators/priors may slightly differ in the implementation from the citation though.
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