Biology 545 - Readings
January 19: Felsenstein 2001. A perspective from the champion of statistical approaches.
Optional: Siddall & Kluge 1997. An example of the arguments made against statistical approaches. It's a long slog; it illustrates the resistance to statistical approaches to phylogenetics, as does the text by Shuh and Brower (2009).
Question for discussion: Why is it that statistical approaches have become dominant?
February 2: Feng & Doolittle 1987. A foundational paper in Progressive Sequence Alignment.
February 16: Nei et al. 1998. The argument is made here that fast methods are frequently sufficient.
March 9: Steel 2005. A short, insightful paper from a brilliant phylogenetic mathematician.
March 30: Goldman 1993. A (perhaps, the) foundational paper in assessing model adequacy.
April 20: Rannala and Yang 1996. One of the original papers on Bayesian estimation of phylogenies.