Complete families of linear invariants for some stochastic models of sequence evolution, with and without the molecular clock assumption.

Abstract excerpt

For various models of sequence evolution, the set of linear functions of the frequencies of the nucleotide patterns forms a vector space, the invariant space. Here we distinguish between the model of nucleotide substitution, and the phylogenetic tree T describing the paths on which these changes occur. We describe a procedure to construct a basis of the invariant space for those models that are extensions of...

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