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Re: Bayesian analysis in phylogeny

Does anyone know some good references I could refer to in order to
become more familiar with it?

The manual... :-}

Has it been applied to morphological data before?

Yes, though only a few times. Wiens, Bonett & Chippindale (2005, Systematic Biology) use it but don't explain how. A trilobite paper from Systematic Palaeontology, IIRC published the same year, explains more, I think. Then there's Müller & Reisz (2006, Systematic Biology) which IIRC gives a fairly adequate explanation.

Does anyone have any practical experience using MrBayes?

Me, very little...