Cao et al. (2000) Gene Phylogeny of Mammals a good example where molecular sequences have led to a big improvement of our understanding of evolution.
Pairwise alignment
Introduction to Bioinformatics
Studies on Oryzias Fishes for Assessment of Environmental Condition
The Origins of Triticum Domestication Ben Grady Dept. of Botany UW-Madison.
Madagascar: need and opportunity Brian Fisher, California Academy of Sciences Madagascar Biodiversity Center.