This will produce one or more trees sorted by topology, summarizing the results of resampling, check Sort topologies under the Consensus Tree Builder options. The frequency of each topology in the set of original trees is calculated and the topologies are sorted by their frequency. A number of these topologies, based on the topology threshold, will be output as summary trees. The summary trees have branch lengths that are the average of the lengths of the same branch from trees with the same topology.
The topology threshold determines what percentage of the original tree topologies must be represented by the summarizing topologies. The most common topology will always be output as the first summary tree. If the frequency (%) of this does not meet the threshold then the next most frequent topology will be added, and so on until the total frequency of the topologies reaches the threshold value.
A topology threshold of 0 will result in only the most common topology being output, a threshold of 100 will result in all topologies being output.