Recombination between nucleotide sequences is a major process influencing the evolution of most species on Earth. While its evolutionary value is a matter of quite intense debate, so too is the influence of recombination on evolutionary analysis methods that assume nucleotide sequences replicate without recombining. The crux of the problem is that when nucleic acids recombine, the daughter or recombinant molecules no longer have a single evolutionary history. All analysis methods that derive increased power from correctly inferring evolutionary relationships between sequences will therefore be at least mildly sensitive to the effects of recombination. The importance of considering recombination in evolutionary studies is underlined by the bewildering array of currently available methods and software tools for analysing and characterising it in various classes of nucleotide sequence datasets. Here we will examine the use of some of these tools to derive and test recombination hypotheses for datasets containing a moderate degree of nucleotide sequence diversity.