Open ruutmdlv opened 1 year ago
treeWAS actually uses phytools' fastAnc function internally to produce the ML reconstructions for continuous phenotypic variables ;)
Great! So, Bayesian methods are not used because they don't give a single output? I'm trying to figure out which is the best way to compute ancestral states.
Thanks again!
Hi Caitie,
What I write here is more of a doubt than an error, which I hope you can help me solve. I am currently using your software and I would like to input the ancestral state reconstruction for the genotype and the phenotype. I have used phytools fastAnc for my continuous phenotype, and an MCMC approach (make.simmap) for the discrete genotype. I have seen that treeWAS also creates the reconstruction using either parsimony or ML, and since I have continuous phenotype, I should use ML. Is it possible to use the phytools output or is it better to use ML?
Best,
Rut