Assessing variability by joint sampling of alignments and mutation rates

When two sequences are aligned with a single set of alignment parameters, o r when mutation parameters are estimated on the basis of a single "optimal" sequence alignment, the variability of both the alignment and the estimate d parameters can be seriously underestimated. To obtain a more realistic im pression of the actual uncertainty, we propose sampling sequence alignments and mutation parameters simultaneously from their joint posterior distribu tion given the two original sequences. We illustrate our method with human and orangutan sequences from the hyper variable region I and with gene-pseu dogene pairs.