Publisher Summary The chapter discusses phylogenetic inference for the analysis of DNA
sequence data. There are five basic steps in the phylogenetic analysis of DNA sequences.
The sequences under study must first be aligned so that positional homologs (the units of
comparison) may be analyzed. Alignment may be straightforward if pairwise differences are
small and most differences result from substitutions but it becomes increasingly difficult as
the sequences become more divergent and insertion/deletion events become more …