Anyone know the best way to visualize conflicting tree toopologies with incomplete overlap in taxon sampling?
What we got: a complete tree (say, species tree), and a whack of gene trees which may or may not have complete taxon sampling. We want a figure with single set of taxon labels that all trees map to. Ignoring edge lengths, as things get messy very quickly. If a gene tree does not contain taxa in the basal split of the species tree, don’t want it’s root to start at the species tree root, but instead more tipward; otherwise, relationships get obscured.
DensiTree is something we have explored, but it doesn’t seem to work well with uneven sampling across trees. We’ve also been playing with R code graciously provided by @liamjrevell, and we may be able to get this to do what we want, but I thought I would check with with the phylo-timaliids to see if something already exists.