This analysis requires only the allelic profiles. Again, individual isolates may be selected or deselected from inclusion using the 'Isolate Selection' dialog reachable from the 'Options' menu. This function creates a distance matrix which assumes no relationships between allele numbers, i.e. each locus difference is treated identically. This is a valid assumption in systems where most genetic variability is brought about by recombination. Distances are calculated for each pair of isolates, where identical isolates have a distance of 0, and those with no loci in common have a distance of 1. For example, in a system with seven loci, if two isolates have four loci differences, their distance is 0.571 (4/7). Output is in NEXUS file format (Maddison et al., 1997) and is suitable for loading into SplitsTree (Huson, 1998; download from here) for split decomposition analysis.
To run the analysis, click 'Analysis ... Lineage Assignment ... Distance Matrix'.
A text editor window will then appear, displaying the distance matrix. 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.