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A Bayesian evolutionary distance for parametrically aligned sequences
Pankaj Agarwal and David States
Journal of Computational Biology 3 (1), 1-17 (1996)
 
TimeTree: a public knowledge-base of divergence times among organisms
S Hedges, Joel Dudley, and Sudhir Kumar
Bioinformatics 22, 2971-2
Presents a really nice system for recovering information about when two species have split. While it may be hard to find a species name that the system recognizes (I did not remember the latin name for "bee" for example), the presentation of the data when it is found is very good.
 
A Comparative Genomic Analysis of Two Distant Diptera, the Fruit Fly, Drosophila melanogaster, and the Malaria Mosquito, Anopheles gambiae
Genome Research 12 (1), 57 (2002)

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