UPGMA (Unweighted Pair Group Method with Arithmetic Mean) (Sneath & Sokal 1973. Numerical Taxonomy. W.H. Freeman and Company, San Francisco, pp 230-234) is a straightforward method of tree construction. Its original purpose was to construct taxonomic phenograms, which are trees that reflect the phenotypic similarities between operational taxonomic units (OTUs). It is generally not considered a good algorithm for construction of phylogenetic trees as it relies on the rates of evolution among different lineages to be approximately equal. In the study of bacterial population biology this is likely not to be the case, so the method should not be relied upon to cluster strains without artefacts. The method uses a sequential clustering algorithm, in which local homology between OTUs is identified in order of similarity, and the tree is built in a stepwise manner. The two OTUs that are most similar to each other are first determined and then these are treated as a new single 'composite' OTU. Subsequently from among the new group of OTUs (composite and simple), the pair with the highest similarity is identified and clustered. This continues until only two OTUs are left. The algorithm assumes that the two most closely related OTUs are more similar to each other than they are to any other. If this is not the case, spurious results may occur. Slightly different clustering may also be seen when the data is presented to the algorithm in a different order. It is important, therefore, not to draw phylogenetic inferences from the clustering pattern seen with this method, although it may prove useful as a quick guide to identifying similar isolates.
The algorithm used here utilises a distance matrix constructed from allelic profile data only. Allele sequences are not used, so each allele number difference is treated identically. This is because in systems involving recombination, a single genetic event, i.e. recombination, may result in a large number of altered sites.
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. To run the analysis, click 'Analysis ... Lineage Assignment ... UPGMA'.
Output is in the form of a tree. Allelic profiles are displayed along with the isolate names. The tree may be saved as a Windows Metafile (WMF) by right-clicking over it with the mouse and selecting 'Save Picture As ...'. This can then be imported into other packages for editing if required.