Relaxed phylogenetics and dating with confidence

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The goal is to estimate the phylogeny as well as the rate of evolution on each lineage based on dates of divergence of their host species.

The first step will be to convert a NEXUS file with a DATA or CHARACTERS block into a BEAST XML input file.

Although we created a taxon set for the ingroup (tmrca(ingroup) in the prior table), we are not going to put an informative prior on this.

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A dialog box will appear allowing you to specify a prior for the MRCA of these three species.Press the small “plus” button at the bottom left of the panel. Rename it by double-clicking on the entry that appears (it will initially be called untitled1).Call it ingroup (it will contain all taxa except the lemur, which will form the outgroup). Since we know that lemur is the outgroup, we will set select the checkbox in the Monophyletic? This will ensure that the ingroup is kept monophyletic during the course of the MCMC analysis.Exactly which options appear depend on whether the data are nucleotides, amino acids, binary data, or general data.The settings that will appear after loading the Primates data set will be the default values so we need to make some changes. For this analysis, we will select substitution models for each partition listed on the left side.

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