The comparison of sequences in order to infer evolutionary relationships is a fundamental technique of bioinformatics. It has a long history in R, too. There are many packages outside of Bioconductor for evolutionary analysis. In the recipes in this chapter, we will take a good look at how to work with tree formats from a variety of sources. A key focus will be how to manipulate trees to focus on particular parts and work with visualizations based on the new ggplot-based tree visualization packages, and the latter's usefulness in terms of viewing and annotating large trees. 

The following recipes will be covered in this chapter:

• Reading and writing varied tree formats with ape and treeio
• Visualizing trees of many genes quickly with ggtree
• Quantifying distances between trees with treespace
• Extracting and working with subtrees using ape
• Creating dot plots for alignment visualization
• Reconstructing trees from alignments using phangorn