After you have aligned a series of sequences, you may wish to use the aligned sequences to infer phylogenetic relationships among the organisms from which the sequences were derived. For a lucid introduction to this topic, visit Stuart Brown's web pages on Phylogenetics: Computing Evolution. Another excellent treatment of this subject is by Brian Golding of McMaster University.
The ExPASy Proteomics tools page has a large collection of links to useful servers and software. Near the bottom of the page is a list of phylogeny servers. PHYLIP is a popular one, and there are a number of PHYLIP servers available on the Web.
If you are interested in pursuing phylogenetic programs in depth, look at Methods in Enzymology, Vol. 266, chapters 20-28. You may also want to get one of the specialized programs for this purpose.
PHYLIP is available from http://evolution.genetics.washington.edu/phylip.html. Here are some examples of PHYLIP output:
PAUP is another major package for phylogenetic analysis. It was written by David Swofford, now at Florida State University. It isn't free, but it's relatively inexpensive. You can find out about it at http://paup.csit.fsu.edu/index.html.