search

caitiecollins / treeWAS

treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes
Other
92 stars 18 forks source link

Ancestral state reconstruction with phytools #66

Open ruutmdlv opened 1 year ago

ruutmdlv commented 1 year ago

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

caitiecollins commented 1 year ago

treeWAS actually uses phytools' fastAnc function internally to produce the ML reconstructions for continuous phenotypic variables ;)

ruutmdlv commented 1 year ago

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!