Phylogenetics is the science of the evolutionary relationships among species. Recently, the term has come to include broader issues such as estimating rates of evolution, dating divergence among species, reconstructing ancestral characters, or quantifying adaptation, all these using phylogenies as frameworks.

Computers seem to have been used by phylogeneticists as soon they were available in research departments [62, 63]. Since then, progress has been obvious in two parallel directions: biological databases, particularly for molecular sequences, have increased in quantity at an exponential rate and, at the same time, computing power has grown at an expanding pace. These concurrent escalations have resulted in the challenge of analyzing larger and larger data sets using more and more complex methods.

The current complexity of phylogenetic analyses implies some strategic choices. This chapter explains the advantages of R as a system for phylogenetic analyses.