TABLE 2.

Kishino-Hasegawa test results of the eleven sequences ambiguously positioned on the phylogenetic tree

Sequencea	Diff −lnLb	Pc
Firstd
168†	67.635	0.000*
197	85.935	0.000*
214	28.094	0.006*
258†	108.153	0.000*
259†	68.407	0.000*
260	2.656	0.344
MF14	29.355	0.005*
PN17	72.269	0.000*
PN21†	35.537	0.002*
PN22	62.599	0.000*
PN23†	66.752	0.000*
Seconde
168	31.741	0.006*
197	51.234	0.000*
214	117.730	0.000*
258	31.743	0.002*
259	25.720	0.035*
260	40.658	0.000*
MF14	116.522	0.000*
PN17	23.612	0.047*
PN21	61.732	0.000*
PN22	20.601	0.092
PN23	27.922	0.019*

^a†, Samples for which endpoint dilutions were performed.

^bThe difference in log-likelihood scores between the best tree for that subalignment against the best tree for the alternative subalignment.

^cThe probability of obtaining that difference in log-likelihoods by chance alone, given that the true trees are identical. *, P values significant at the 0.05 level. Note that, to be conservative, we only identify a sequence as a putative recombinant if both subalignments produce trees that are mutually (statistically) different.

^dThe subalignment of sequences using the query sequence before the putative crossover point identified by RIP.

^eThe subalignment of sequences using the query sequence after the putative crossover point identified by RIP.