**2.4 Analysis of results obtained by molecular epidemiology**

Comparison and interpretation of raw data generated by molecular typing methods, such as gel electrophoresis band patterns, sequence alignments, or hybridization matrix patterns could be performed by visual analysis when there are few strains. However, if the analysis includes many strains, the comparison turns out to be very difficult. Therefore computer programs have become indispensable in molecular epidemiological investigations.

Computer programs that compare band sequences or patterns employ clustering algorithms that can generate dendrograms or trees illustrating the arrangement of the clusters produced. For pattern recognition, such as electrophoretic banding patterns or hybridization matrices, additional programs are needed to capture, digitize, and normalize the patterns.

There are different commercially available platforms for databasing and gel analysis that have been developed for computer-assisted analysis such as BioNumerics, GelCompar (Applied Maths, Sint-Martens-Latem, Belgium), Diversity Database Fingerprinting Software (Bio-Rad Laboratories, Hercules, Ca). Treecon (Van de Peer and De Wachter 1994).
