This command is used to specify breaks in your input data matrix. Your data may be a mixture of genes or a mixture of different types of data. Some of the models implemented by MrBayes account for nonindependence at adjacent characters. The autocorrelated gamma model, for example, allows rates at adjacent sites to be correlated. However, there is no way for such a model to tell whether two sites, adjacent in the matrix, are actually separated by many kilobases or megabases in the genome. The databreaks command allows you to specify such breaks. The correct usage is:
databreaks <break 1> <break 2> <break 3> ...
For example, say you have a data matrix of 3204 characters that include nucleotide data from three genes. The first gene covers characters 1 to 970, the second gene covers characters 971 to 2567, and the third gene covers characters 2568 to 3204. Also, let's assume that the genes are not directly adjacent to one another in the genome, as might be likely if you have mitochondrial sequences. In this case, you can specify breaks between the genes using:
databreaks 970 2567;
The first break, between genes one and two, is after character 970 and the second break, between genes two and three, is after character 2567.