TABLE 2.

Results of Shimodaira-Hasegawa test of log-likelihood scores of phylogenetic trees from 16 HIV-1 sequence alignment partitions^a

Topology	% Difference in log-likelihood scores between indicated topology and partition:
	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	Full
1	Bestb	0.7209	1.1930	1.9674	2.1753	2.2974	2.3512	2.6015	2.7271	2.7048	2.6335	2.7620	2.5882	2.6108	2.5713	2.5361	1.3891
2	0.5185	Best	0.2557	0.9859	1.1623	1.2799	1.7866	2.1588	2.6553	2.6878	2.5347	2.5648	2.3750	2.3361	2.1135	2.0083	1.1230
3	1.0678	0.5327	Best	0.6109	0.8745	0.9897	1.5571	2.4391	2.9920	2.9947	2.7849	2.9575	2.7233	2.7536	2.5049	2.4218	1.3669
4	1.0561	0.7319	0.2932	Best	0.2855	0.4307	0.8002	1.6009	2.5731	2.7184	2.5613	2.7427	2.6035	2.6045	2.4672	2.4265	1.2074
5	1.5933	1.0578	0.5012	0.2280	Best	0.0630	0.7739	1.6692	2.5656	2.7227	2.6942	2.9002	2.6727	2.7123	2.6138	2.5240	1.3184
6	2.0691	1.5322	0.8054	0.5802	0.2133	Best	0.5049	1.4456	2.3298	2.5709	2.4989	2.7465	2.5415	2.7267	2.5447	2.5870	1.3661
7	2.0241	1.9965	1.6533	1.3221	0.9574	0.6126	Best	0.4764	1.3834	1.6688	1.8100	2.3133	2.2885	2.4053	2.2186	2.1311	1.1313
8	2.0890	2.2356	2.2325	1.9515	1.5627	1.2564	0.4859	Best	0.7663	1.0350	1.2561	1.8467	2.1894	2.4730	2.2735	2.2648	1.1607
9	2.3840	2.7783	2.9452	3.0665	2.6967	2.3794	1.3562	0.5137	Best	0.2814	0.6077	1.2922	1.6419	2.4848	2.4826	2.3586	1.2749
10	2.3853	2.7809	2.7679	3.0004	2.5331	2.2114	1.1801	0.5814	0.1744	Best	0.3394	0.9424	1.2240	1.9605	2.0840	2.0594	1.0873
11	2.0515	2.3241	2.4578	2.7522	2.5574	2.3529	1.6246	1.0726	0.6188	0.3250	Best	0.4112	0.5662	1.1464	1.3853	1.6641	0.8758
12	1.9734	2.3448	2.4497	2.7742	2.7011	2.5509	2.0917	1.6131	1.1423	0.7546	0.2168	Best	0.0246	0.5643	0.7589	1.1675	0.7813
13	2.1229	2.4303	2.5165	2.8453	2.7626	2.6427	2.4491	2.3765	1.9560	1.5132	0.9095	0.5765	Best	0.5025	0.7633	1.1289	1.0132
14	2.3206	2.7398	2.8867	3.2141	3.1136	2.9320	2.7095	2.7783	2.7982	2.3112	1.4976	1.0486	0.4448	Best	0.3187	0.7565	1.1685
15	2.0514	2.3911	2.4271	2.8182	2.6858	2.4941	2.2069	2.2631	2.4310	2.1594	1.4966	1.2172	0.6932	0.3354	Best	0.3885	0.9242
16	2.2006	2.5360	2.5980	2.9949	2.8646	2.6873	2.3829	2.5254	2.6265	2.4253	2.0910	1.7298	1.2809	0.8847	0.3880	Best	1.0002
Full	0.7028	0.8927	0.8995	1.1256	1.0281	0.9316	0.5759	0.5808	0.6830	0.6131	0.4665	0.5974	0.5677	0.6368	0.4246	0.3091	Best

^aFull, full-length alignment. Different fonts indicate significance: boldface, P < 0.001; underline, P < 0.01; italic, P < 0.05; roman, not significant.

^bBest indicates the comparison of trees generated from the same data.