Clustering phylogenetic loci: estimating number of clusters (treeCl)

Question

[Harry Detering]

When analyzing larger sets of phylogenetic loci, incongruences between different sets of loci with distinct evolutionary histories (e.g. by hybridization, horizontal gene transfer, incomplete lineage sorting) can confound the reconstruction of phylogenetic relationship. One approach to tackle the problem is to split the loci into clusters that support the same history.

A tool that implements clustering of locus by inter-tree distances is treeCl. The paper describes a method to estimate the most likely number of clusters, however the documentation of the software is rather minimal. Has anyone used their method to estimate the number of clusters from the data and would be willing to share their approach?

Thanks a lot - Harry