TreeChopper clusters tree leaf nodes according to phylogenetic distance.A graph is constructed from the tree like so: all leaves are visited, and from each leaf, all neighboring leaves within a specified distance threshold are added to a graph with an edge placed between them. After building this graph, each edge connecting pairs of nodes is examined and a Jaccard similarity coefficient is computed. Those edges that loosely connect nodes as defined by this similarity coefficient are removed. The nodes connected by the remaining edges are clustered by transitive closure (single linkage clustering) and reported as OTUs.
The Broad Institute, Cambridge, MA
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