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Survey philosophical piece on phylogenetic inference:

The piece we are reading by Matt Haber is a direct response to the following:

The Farris piece below is perhaps the most famous piece defending the Parsimony method. The Felsenstein is the first two chapters from Inferring Phylogenies and describes the Parimony method in a very clear way.

Foster is an attempt to make more perspicuous what is going on. Howson and Urbach is a short, general introduction to Bayesian reasoning, the Lewis piece is a survey of some work in phylogenetics including Bayesian methods and the Velasco piece is a very basic introduction to Bayesian methods in phylogenetics, but is a more philosophical piece which discusses the assignent of prior probabilities to trees.