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Background: A basic problem of molecular evolution is to describe the natural selection on DNA sequence.So-called codon model is widely used to describe this selection force acting on protein coding region by calculating the ratio of synonymous to non-synonymous substitutions.However, many studies has identified functional RNA conserved structure, the effect of RNA structure selection is ignored in these models.Here we present a (new model) to introduce empirical RNA structure selection information into classical phylogenetic analysis framework, which would provide a better understanding selection pressure influence on RNA secondary structure.