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I have data for 5 individuals of 15 lineages (normalized gene expression, 75 total samples), a phylogeny, and would like to calculate the maximum likelihood under brownian motion, then compare the result to a model with selection (i.e. an Ornstein Uhlenbeck model) while retaining information about within species variation.

Does anyone know a program that could help me do this? Using EVE (Rohlfs et al. 2015), I'm able to calculate the likelihoods of the OU model, but not under brownian motion.

Thanks!

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  • $\begingroup$ Improve the description of the question. What kind of data you have for each individual? When you say you "would like to calculate the maximum likelihood", but the ML of what specifically? Do you mean compare the fit of BM and OU models? Since you mentioned EVE, I'm assuming you have data on gene expression. Notice that a BM is a special case of a OU model with alpha=0. $\endgroup$ – Diogo B Provete May 2 '17 at 15:17
  • $\begingroup$ You're correct that it is gene expression data. I would like the ML of the data under a fit model of brownian motion, then compare to multiple OU models using AIC. I am aware that BM is a special case of OU, but the issue is I can't figure out how to constrain alpha to 0 (or make it negligibly small) within EVE $\endgroup$ – Jautis May 3 '17 at 16:09

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