The percent identity plots in GeneDoc are an alternative to tables showing the percentage of sequence residues that are identical in every pair of sequences in the alignment. Such tables have often been published as a way to describe the degree of divergence among the sequences in the alignment. This has been a useful guide to the probable amount of information available in the alignment and robustness of the alignment.
More divergent sequences make the alignments more informative but also less robust and reliable.
The data in these plots can be either strict identities or the count conservative or favorable substitutions as if they were also identical residues. In this context empirical refers to the fact that the plot is experimental, or empirical, data rather than derived from a mathematical equation describing a theoretical distribution such as the gaussian distribution. The plot is created by first sorting the data to be plotted into ascending order. Then for each data point you compute the fraction of data points that have the same or a smaller value. The data is then compressed to eliminate multiple points that have the same data value.