My view here is that noone in their right mind should be using P-values - Evalues are a much more sensible statistic. I think the only thing which actually produces just P-values is BLAST 1 series (am I wrong?) and I think we should just document that we put the Pvalue in the Evalue slot as it is also 10 year old software now and people should have moved on from the BLAST 1 series by now.