Table 1.

Comparison of maximum likelihood phylogenetic tree with hypotheses consistent with within-patient viral evolutiona

ConstraintLog likelihoodDecrease in likelihoodStandard deviationP valueExpected likelihood wt
SHAU
Best tree−3,658.760.00NANANA0.99
All 5 MLV 2010−3,721.2262.4614.92<0.001<0.0001<0.0001
MLV001 2010−3,689.9331.179.620.001<0.0001<0.0001
MLV002 2010−3,696.6637.9010.800.002<0.0001<0.0001
MLV003 2010−3,679.7320.969.310.0220.0020.0086
MLV005 2010−3,687.6228.8610.150.0040.00030.0004
MLV006 2010−3,701.6342.8712.900.002<0.0001<0.0001
• a The most stringent constraint involved all 5 MLV sequences from the second time point, while each of the 5-s time point sequences was also constrained individually to cluster with the CFS type 1 sequence from the first time point. The trees were compared using pairwise Shimodaira-Hasegawa (SH) tests, the approximately unbiased (AU) test, and expected likelihood weights. All of the constrained trees were significantly worse than the maximum likelihood tree. NA, not applicable.