ELynx.MarkovProcess.GammaRateHeterogeneity

Creation date: Thu Feb 28 14:09:11 2019.

At the moment, a mixture model is used to emulate gamma rate heterogeneity. This does not come with huge run time increases when simulating data. For inference however, it would make a lot of sense to reuse the Eigendecomposition for all rate heterogeneity components though.

Documentation

summarizeGammaRateHeterogeneity :: Int -> Double -> [ByteString]

Short summary of gamma rate heterogeneity parameters.

expand :: Int -> Double -> PhyloModel -> PhyloModel

For a given number of rate categories, a gamma shape parameter alpha and a substitution model, compute the scaled substitution models corresponding to the gamma rates.