Topology | Likelihood score for data set | |
---|---|---|

cagA | vacA | |

cagA tree | −14,893.50 | −18,862.81* |

vacA tree | −16,922.57* | −17,537.20 |

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*a*Data set denotes the alignments of the*vacA*and*cagA*genes. Topology denotes the maximum-likelihood trees shown in Fig. S6 in the supplemental material. The likelihood scores (−lnL) are shown in the table and are based on comparing each data set across its own ML tree topology and the alternative topology. The lowest (best) likelihood scores are indicated in boldface for each data set. Significance of the likelihood differences from the comparisons of a common data set across different topologies was measured using a bootstrap approach with RELL sampling and full optimization for 1,000 replicates. For example, the score from the comparison of the*cagA*data set against the*cagA*topology (−14893.50) is significantly better than the score from the alternative comparison of the*cagA*data set against the*vacA*topology (−16922.57). *,*P*< 0.001