The phangorn package is a relatively new package in R for the analysis and comparison of phylogenies. See here for the Bioinformatics paper and here for the package. Here is an example of using phangorn from getting sequences to making phylogenies and visualizing them:

Getting sequences from Genbank

Multiple alignment

Maximum likelihood tree reconstruction

Visualizing trees

Visualizing trees and traits
Make fake traits:

Visualize them on trees: