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.

Please cite THIS paper if you use SDM.

Running SDM

SDM uses a PHYLIP-like interface (Felsenstein, 1993). The user is asked for the name of the input file.
This input file contains either a collection of k distance matrices in PHYLIP format (lower triangular or square), or a collection of k trees with branch lengths (rooted or unrooted, binary or non-binary, but non bootstraped) in NEWICK format. The value of k must be given before the collection. Comments can be written inside the input file if the line begins with the '%' character.

Here is an example of input file containing square distance matrices:
SDM matrice example
Here is an other input file containing trees:
SDM trees example
SDM outputs several files: SDM also provides the deformed source matrices, when option (4) is checked (see below); the corresponding file is called sdm_deformed_matrices.

To run SDM on LINUX, use the command:
java -jar SDM.jar
To run SDM on WINDOWS, double-click on win_SDM.bat

PHYLIP-like interface

A PHYLIP-like menu display the various options:

SDM PHYLIP-like interface