Sequence similarity: why are we interested in, how do you define it Scoring metrics: what is important in similarity
Scoring with DNA: integrating biological knowledge
Scoring with proteins: integrating biological knowledge
PAMs and BLOSUMs: the marriage of statistics and biology Gaps: how strong do they count?
Constant, affine and concave gap penalties
The dynamic programmig trick
Global versus local
Heuristics to get some speed
Can we trust our alignment?
PSI-BLAST & Co: highlights and traps
Multiple Sequence Alignment: finding and scoring them The third dimension
From alignments to trees