Bootstrap confidence levels for HIV-1 recombination

Recombination has been invoked to explain the disparate evolutionary relationships observed for different genes or sequence segments of a single HIV-1 genome. We present a new method of assessing confidence in HIV-1 recombination as an alternative to the segment-by-segment nonparametric bootstrap commonly applied to confirm HIV-1 recombinant data. Our new method uses the bias-corrected accelerated percentile interval (BCa) bootstrap method as applied to the "problem of regions" (Efron and Tibshirani 1998). It is an extension of the BCa method used in the inference of evolutionary relationships (Efron et al. 1996). This method has two advantages over the traditional bootstrap procedure: (1) it gives a single overall confidence measure rather than segment-by-segment results, and (2) it is more accurate. We test our method on 61 sequences, including 16 with ambiguous recombinant status.