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over a longer period of evolutionary time. Each amino acid is more or less likely to mutate into various other amino acids. For instance, a [[hydrophilic]] residue such as [[arginine]] is more likely to be replaced by another hydrophilic residue such as [[glutamine]], than it is to be mutated into a [[hydrophobic]] residue such as [[leucine]]. (Here, a residue refers to an amino acid stripped of a hydrogen and/or a [[hydroxyl group]] and inserted in the [[polymer|polymeric chain]] of a protein.) This is primarily due to redundancy in the [[genetic code]], which translates similar codons into similar amino acids. Furthermore, mutating an amino acid to a residue with significantly different properties could affect the [[protein folding|folding]] and/or activity of the protein. There is therefore usually strong selective pressure{{dubious|date=October 2014}} to remove such mutations quickly from a population.
If we have two amino acid sequences in front of us, we should be able to say something about how likely they are to be derived from a common ancestor, or [[Sequence homology|homologous]]. If we can line up the two sequences using a [[sequence alignment]] algorithm such that the mutations required to transform a hypothetical ancestor sequence into both of the current sequences would be evolutionarily plausible, then we'd like to assign a high score to the comparison of the sequences.
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