ABSTRACT
In this chapter, a practical guide for carrying out sequence similarity searches of databases, multiple sequence alignments, and molecular tree building is presented. Background information is available in a number of articles and books. 1•5 The services and programs that have been developed for computer analysis of sequence data are designed for the convenience of the user. However, access to these systems requires not only being properly connected electronically, but having some understanding of how to tell either a program or a service what you want to achieve. Initially, a first-time user may not have a clear understanding of the criteria that have been used to generate the data by various analytical procedures. With some experience, however, the output of the various programs becomes comprehensible. Generally, the on-line services have good documentation and provide references to key articles in the literature.
