The Web site for the text: An Introduction to Bioinformatics Algorithms
This links to a course Web site at Washington University, Bio 5495/BME 537, Computational Molecular Biology. The course is a survey of algorithms and methods in computational molecular biology. Topics covered include sequence alignment algorithms, multiple sequence alignment, RNA structure prediction, motif and pattern searches, and phylogenetic inference.
This links to another course Web site at Stanford, CS 262 Handouts of Computational Genomics
A whole lot of bioinformatics links
Some pretty nice tutorials on Basic Bioinformatic Analysis