Sequence comparisons (Bioinformatics?)

In the thread "Is convergent evolution evidence against common descent?" the topic of comparing genetic and protein sequences came up:(Message 138)This is, of course, relevent to that topic but it turns out there is enough information and resources on the web to have some fun with this. This topic is to spin off this area alone from the convergent topic.The ClustalW form at http://align.genome.jp/ , allows for comparisons to be made.I would like this topic to contain explanations (in considerable detail) of what is done by the program at that site and more on how to use it.We can also offer up questions about and examples of sequence comparisons here.

Thread copied to the Sequence comparisons (Bioinformatics?) thread in the Biological Evolution forum, this copy of the thread has been closed.