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Change in nucleotide sequence as a function of time, or in RNA or protein function.
Molecular evolution is phenotypic or genotypic evolutionary change specifically as it can be observed at molecular levels or in molecular terms. This includes in terms of phylogenetic analysis as well as experimental evolution studies.
The concept of homology is used in the study of molecular evolution literally to the point that the concept is abused! Indeed, it is not just standard practice to search for homologies among sequenced genes but hugely automated searches for similarity in base or amino acid sequence are routinely performed. Resulting from these efforts the function of otherwise uncharacterized genes and proteins often are assigned functions based solely on these similarities.
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