SDM: a Fast Distance-based Approach for (Super)Tree Building in Phylogenomics.
Criscuolo A., Berry V., Douzery E.J.P., Gascuel O. Systematic Biology. 2006 55(5):740-755.
paper if you use SDM.
Super Distance Matrix from multi-gene datasets
SDM is a new method to combine distance matrices (or trees with branch lengths). This method involves deforming the different matrices, without modifying their topological message, to bring them as close as possible to each other. A distance supermatrix is then computed by averaging the deformed source matrices. When this supermatrix is complete, any tree building algorithm can be used to obtain the supertree that summarizes the input distance matrices (or trees with branch lengths); e.g. BioNJ
(recommended). With incomplete matrices just a few algorithms are applicable. We recommend using MVR* from our PhyD*
package. MVR* not only inputs the distance supermatrix, but also a matrix (computed by SDM) containing the variances of the distance estimates in the supermatrix. Using MVR* is also a relevant option with complete supermatrices, as MVR* benefits from the additional knowledge contained in this variance matrix..