Measurement of Selection on RNA molecules

When analyzing protein coding genes it is very useful to measure the strength of selection. Genes that are not selected are often non-functional (pseudo genes). For selected genes, the strength and distribution along the sequence often gives functional clues to what the coded protein does and which positions are important. The most used such measure is the Ka/Ks ratio that measures the relative amounts of amino acid changing versus not amino acid changing nucleotide substitutions. There is not an analogue of this for RNA molecules and the aim of this project is to consider this.