Tabulate or define frequencies of characters For likelihood calculations it is necessary to define the equilibrium frequencies of characters. In most cases we will estimate these from the data, often by simply using the observed empirical frequencies. The statement HarvestFrequencies (obsFreqs, myFilter, 1, 1, 1); tabulates the nucleotide frequencies in myFilter and stores them in a vector named obsFreqs. Had we wanted to use different frequency values for some reason, HarvestFrequencies statement would simply have been replaced with something like myFavoriteFreqs = {{.10}{.40}{.20}{.30}}; This statement would create a vector named myFavoriteFreqs with elements 0.10, 0.40, 0.20, and 0.30. myFavoriteFreqs could be used just like the variable obsFreqs.
Sergei L. Kosakovsky Pond and Spencer V. Muse, 1997-2002