A comprehensive workflow for supertree and supermatrix approaches applied to DNA data. In the supertree approach, phylogenetic trees are reconstructed for each of the five genes. The resulting source trees are recoded using the Baum Ragan coding to obtain the MRP matrix. Based on this matrix the species tree is computed using MRP parsimony. The supermatrix approach takes the concatenated gene alignments and computes the species tree directly using standard tree reconstruction methods.
von Haeseler BMC Biology 2012 10:13 doi:10.1186/1741-7007-10-13