Why are only the first 30 OTUs are shown in the dendrogram?
By default, a maximum of 30 OTUs are displayed on each page of the dendrogram. To display additional pages or to change the number of OTUs/page, right-click on the plot to bring up the options window. You can change many aspects of the plot including the fonts used to display the titles and OTU labels. In version 2.1 you can use the PageUp and PageDown keys to scroll through the other pages. You can also use the “+” and “-” keys to change the number of OTUs per page.