Solution phylogeny

Sequence-based phylogenies are determined using an parsimony algorithm (Cedergren al.. 1988). Most parsimonious solutions are evaluated using a bootstrapping technique and occasionally branch points are validated by the invariants method of Cavender and Felsenstein (1987) and of Lake (1987). 

As we have seen, the true justification of any method of minimum evolution lies in an appeal to a probability model and the primitive notion of likelihood, and to that extent is closer to the method of least squares than to the methods of mathematical physics. A matter of minor historical interest is that the first attempt at a statistical solution of the phylogeny problem did in fact invoke least-squares ... 

Charleston, M.A., Jungles a new solution to the host/parasite phylogeny reconciliation problem, Math. BioscL, 149, 191-223, 1998. 

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