r package for downstream analysis of phylogenetic trees

Question

[TM]

I have built a phylogenetic tree in r with phangorn and other useful packages. However, I have not been able to find any package for downstream analysis. For example, I would like to identify at which point on the tree each mutation occurs while taking into account the ambiguity in the reconstruction of unobserved sequences. Is there any tool for this kind of analysis, or should I write codes by myself? This is my first post here in Biostars. Any advice would be appreciated. Thank you in advance