Abstract
Inferring the evolutionary relationships among related taxa (species, genera, families, or higher groupings) is one of the most fascinating problems of molecular genetics [11, 13, 14]. It is now relatively simple to sequence genes and to compare the results from several contemporary taxa. In the current chapter we will assume that the chore of aligning the DNA sequences from these taxa has been successfully accomplished. The taxa are then arranged in an evolutionary tree (or phytogeny) depicting how taxa diverge from common ancestors. A single ancestral taxon roots the binary tree describing the evolution of the contemporary taxa. The reconstruction problem can be briefly stated as finding the rooted evolutionary tree best fitting the current DNA data. Once the best tree is identified, it is also of interest to estimate the branch lengths of the tree. These tell us something about the pace of evolution. For the sake of brevity, we will focus on the problem of finding the best tree.
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