Methods for inferring phylogenies from nucleic acid sequence data by using maximum likelihood and linear invariants.

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Abstract
Likelihood methods and methods using invariants are procedures for inferring the evolutionary relationships among species through statistical analysis of nucleic acid sequences. A likelihood-ratio test may be used to determine the feasibility of any tree for which the maximum likelihood can be computed. The method of linear invariants described by Cavender, which includes Lake's method of evolutionary parsimony as a special case, is essentially a form of the likelihood-ratio method. In the case of a small number of species (four or five), these methods may be used to find a confidence set for the correct tree. An exact version of Lake's asymptotic chi 2 test has been mentioned by Holmquist et al. Under very general assumptions, a one-sided exact test is appropriate, which greatly increases power.

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