This package includes a modified version of dnapars.exe from Phylip 3.6. The orignal dnapars,exe uses a menu for settings of parameters. I changed it into a command-line driven one, called mbetoolbox_dnapars.exe. Then I built a MATLAB interface for it. Within MATLAB, after setting the path, set you may type:
1) >mbetoolbox_dnapars, or
2) >mbetoolbox_dnapars(seq_no)
where species_no is an integer indicating how many sequences in your input file. The input file is an aligned DNA sequences in Phylip format and should be named 'InFile'.