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 GenbankMultiple alignmentMaximum likelihood tree reconstructionVisualizing treesVisualizing trees and traitsMake fake traits:Visualize them on trees: