and the sense codons (i.e., the 61 codons that encode amino acids in the standard genetic code) for aligned protein-coding gene sequences. In fact, substitution models can be developed for any biological characters that can be encoded using a specific alphabet (e.g., amino acid sequences combined with information about the conformation of those amino acids in three-dimensional protein structures). The majority of substitution models used for evolutionary research assume independence among sites (i.e., the probability of observing any specific site pattern is identical regardless of where the site pattern is in the sequence alignment). This simplifies likelihood calculations because it is only necessary to calculate the probability of all site patterns that appear in the alignment then use those values to calculate the overall likelihood of the alignment (e.g., the probability of three "GGGG" site patterns given some model of DNA sequence evolution is simply the probability of a single "GGGG" site pattern raised to the third power). This means that substitution models can be viewed as implying a specific multinomial distribution for site pattern frequencies. If we consider a multiple sequence alignment of four DNA sequences there are 256 possible site patterns so there are 255 degrees of freedom for the site pattern frequencies. However, it is possible to specify the expected site pattern frequencies using five degrees of freedom if using the Jukes-Cantor model of DNA evolution, which is a simple substitution model that allows one to calculate the expected site pattern frequencies only the tree topology and the branch lengths (given four taxa an unrooted bifurcating tree has five branch lengths). Substitution models also make it possible to simulate sequence data using Monte Carlo methods. Simulated multiple sequence alignments can be used to assess the performance of phylogenetic methods and generate the null distribution for certain statistical tests in the fields of molecular evolution and molecular phylogenetics. Examples of these tests include tests of model fit and the "SOWH test" that can be used to examine tree topologies. Application to morphological data The fact that substitution models can be used to analyze any biological alphabet has made it possible to develop models of evolution for phenotypic datasets (e.g., morphological and behavioural traits). Typically, "0" is. used to indicate the absence of a trait and "1" is used to indicate the presence of a trait, although it is also possible to score characters using multiple states. Using this