Table 2.

Insertion/deletion rates among different phylogenetic groups estimated in rate variation model. Estimation was based on the select-genes trees.

Group	Taxa	Genome Size	Branch Length	Rate Variation			Constant Rate		ΔLnL
				α value	MLE	LnL	MLE	LnL
Bacillus	13	4.9	0.126886	0.39	4.79	-40187	0.51	-40545	358*
Brucella	4	2.1	0.000775	0.053	126.82	-1214	22.77	-1253	39*
Burkholderia	7	3.8	0.028971	0.35	25.58	-17258	3.54	-17717	459*
Candidatus	4	1.3	0.608223	∞	0.36	-4635	0.36	-4635	0
Chlamydophila	7	1.2	0.081640	0.41	0.36	-1427	0.22	-1451	25*
Clostridium	5	3.3	0.123806	0.50	11.93	-9544	9.84	-9769	225*
Corynebacterium	5	3.0	0.172207	0.79	2.48	-8537	0.71	-8600	63*
Ehrlichia	5	1.5	0.059080	∞	0.27	-832	0.27	-832	0
Escherichia	7	5.0	0.002852	0.23	51.34	-10689	12.53	-11236	547*
Helicobacter	5	1.7	0.232504	0.47	1.75	-3966	1.16	-4133	167*
Lactobacillus	6	2.2	0.250368	∞	0.44	-9302	0.44	-9302	0
Mycobacterium	6	4.2	0.070373	0.41	19.94	-14693	1.63	-14718	25*
Mycoplasma	12	0.9	0.441286	∞	0.13	-8448	0.13	-8448	0
Prochlorococcus	5	1.9	0.356990	2.42	0.17	-4414	0.15	-4421	7*
Pseudomonas	8	6.3	0.057175	1.66	2.09	-27117	1.32	-27231	114*
Rhodopseudomonas	4	5.3	0.060450	0.59	2.73	-9342	1.43	-9433	91*
Rickettsia	5	1.3	0.055962	0.33	3.70	-3172	1.30	-3302	130*
Salmonella	5	4.8	0.002930	0.37	12.19	-5283	7.97	-5356	73*
Shigella	6	4.6	0.003188	0.37	39.69	-9753	16.25	-10064	311*
Staphylococcus	13	2.8	0.034391	0.090	407.56	-12283	19.77	-14514	2231*
Streptococcus	19	2.0	0.041459	0.34	12.76	-24015	9.39	-26146	2131*
Synechococcus	5	2.6	0.364362	∞	0.31	-7320	0.31	-7320	0
Vibrio	5	3.2	0.104170	0.21	11.72	-8623	0.74	-8883	260*
Xanthomonas	6	5.1	0.024790	0.33	18.00	-9388	3.21	-9714	326*
Yersinia	6	4.6	0.000263	0.064	261.75	-3236	46.77	-3606	370*

*Significant improvement