In Chapter - Generating Random Sequences we combine randomization with statistical analyses to test the accuracy of our algorithms and hypotheses. By creating random amino acid sequences and feeding these as input to our programs for phylogenetic trees, we can obtain expected values and variances for the random cases. Comparing these results to the values for actual sequences, we can conclude that the results from our algorithms are either marginal, significant or insignficant.
There are many built-in Darwin tools for creating graphical representations of standard statistical objects such as dot plots and histograms. We introduce these functions here and discuss the system variables associated with these routines.
We also present the basic functions for creating pictures of binary trees. The more specific options associated with these functions are omitted from this discussion and introduced in Chapter - Phylogenetic Trees where we use them extensively.