Domain frequencies are assessed from two different viewpoints. The first viewpoint considers how many “copies” of a particular domain are necessary to construct all the representative proteins. Frequencies are computed as the number of instances of a domain divided by the total number of domains over all representative proteins; they sum to 1 and can thus be presented as a waffle chart (generated here using the python pywaffle package [81]). The second viewpoint considers how many of the representative proteins contain a particular domain at all. Here, frequencies are computed as the number of representative proteins with one or more copies of the domain, divided by the number of representative proteins. These frequencies are presented as bar charts.

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