Could we have an idea about the relative importance of gene saturation vs selection pressure for explaining incongruent topologies for a given taxon between different gene sequences?
Yes, I've been working on the problem of estimating gene saturation as a cause of incongruence over the last several years.
Article PhyDesign: An online application for profiling phylogenetic ...
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Article Profiling Phylogenetic Informativeness
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Article Phylogenetic Signal and Noise: Predicting the Power of a Dat...
...how you compare saturation to selection depends on what you mean by selection... do you mean selection for molecular convergence?
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