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The CD8(+) T cell response is important in the control of many viral and other infections. There have been many studies aimed at better understanding the influence of T cell receptor diversity on immune responses and the evolution of the T cell receptor repertoire over time and through the various stages of immune responses to infection. In recent years, there has been an increase in both the number of studies using T cell receptor data and the volume of T cell receptor data generated per study. Appropriate analytical tools are required to analyse this data. We present a robust approach to assessing the similarity between samples of the T cell receptor repertoire, which we demonstrate on published data of subsets of the influenza A virus (DNP366)-N-b- and D(b)PA(224)- specific CD8+ T cell responses in mice sorted on the expression of CD62L, which is a marker distinguishing central and effector memory cells. (C) 2007 Elsevier B.V. All rights reserved.