SDM (super distance matrix ) 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 or FastME (recommended).
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“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.