Once a single-locus sequence file has been loaded, sequences may be converted to the NEXUS file format (Maddison et al., 1997), suitable for loading into SplitsTree (Huson, 1998; download from here). Individual sequences may be selected or deselected for inclusion in the output file by selecting 'Allele Selection' on the 'Options' menu. To start the conversion, select 'Sequences to NEXUS format' on the 'Convert' menu.
A text editor window will then appear, displaying the sequences in NEXUS format. This is editable if required and text may be copied or pasted using standard Windows functions. Clicking on the Save button will bring up a standard save file dialog window.