Dear ladies and gentlemen! Please tell me if I calculate Tajima's D values for each gene in the operon while some gene has disappeared. How correct is it to add empty lines in multiple alignments, making the number of lines the same in all multiple alignments? It is clear that this will decrease \theta _{w}, and thus the Tajima'D value itself will increase, but these are real data on the analyzed population.

To what extent is such reasoning correct?