Abstract
In Drosophila melanogaster there are significant differences in the way the polytene chromosomes are arranged in different nuclei from the same salivary gland. Visual inspection of the models of these nuclei was inadequate to delineate all of the features conserved in their structures. To bypass this limitation, models of these nuclei were constructed in a format compatible with computational manipulation. By applying some simple algorithms to these models, quantitative comparisons were made which revealed otherwise cryptic features common to many nuclei. Given here are the details of several algorithms for describing and comparing the arrangement of the chromosomes within the nuclei.