Hello, everyone! Recently, I was reading manuals of P4
software about testing compositional homogeneity on the data.
The author assumes Tree and model based composition test
works the best.Now I have three puzzles: 1) Which fixed tree should
be used for this test? Is this tree the best tree generated by
the homogeneous model using Bayesian MCMC? 2) Is the
homogeneous model the best fit model suggested by software
such as Protest of Modelgenerator? 3) How to carry out these
steps using P4, Can anyone provide scripts kindly? Any answer
will be appreciated. Thanks!
I'm not an expert, but I would suggest you to consider other methods. I haven't tested them, but you can try if they work and if they are "friendlier". Firstone isn'specific for you domain, but could be illuminating.
Sorry if I have not answered to your specific questions, but a suggestion can be useful
Good Luck
Thanks very much for your suggestions! The articles provided by you is quite useful for me, I will read them later!
I am the author of P4. When speaking of "compositional homogeneity" or "compositional heterogeneity" we need to be clear about whether we are talking about homogeneity over the tree (or over time, or over taxa), or over the data. The Elhaik and Graur software IsoPlotter suggested by Davide F Castaldi addresses the latter, that is heterogeneity over the data. The Liu et al study and the Luo study both used the NDCH model as implemented in p4, and addressed compositional heterogeneity over the tree. Is that what the original poster had in mind?
To clarify my opinion for the original poster, I do not assume that the tree and model based composition fit test that I described there works the best. It has advantages over simpler tests, and is really a model fit test, and so is more general than a compositional homogeneity test. Both the Liu et al study and the Luo study used an MCMC, using posterior predictive simulations, which I would recommend over the tree and model based composition fit test. P4 comes with a lot of documentation and examples to show you how to do that, but you can use other software.
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