Supporting material

• Sean Eddy on scoring matrices in Nature Biotechnology.
• Sean Eddy on dynamic programming for pairwise alignments, in Nature Biotech, 2004.
• NCBI on significance. Have NCBI's experts explain the significance of scores to you.
• Anders Krogh on HMM methods. Using HMM:s for modeling protein domains and gene finding.
• Untapped Bounty: Sampling the Seas to Survey Microbial Biodiversity by Liza Gross. A nice introduction to applications of Bioinformatics.
• Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes by Rasmussen and Kellis, Genome Research, 2007.