**1. Introduction**

Comparative analyses of haplotype sequences allow many efficiencies. It is not surprising that there are many enthusiastic claims. Haplotypes, by any of many definitions, offer opportuni‐ ties to understand the inheritance of polymorphic traits and their regulation. The most useful are markers of extensive complex polymorphic sequences of evolutionary significance even when the functional components, whether coding or noncoding, are yet to be elaborated.

Substantial advances became possible with the elucidation of genomic structure and function more than 20 years ago and long before recent advances in sequencing technology [1] and bioinformatics [2]. It became clear that haplotypes, *not genes*, can be regarded as the principal unit of inheritance.

This chapter evaluates some competing strategies and illustrates the power now available through NGS.

© 2015 The Author(s). Licensee InTech. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
