Bootstrap, Bayesian probability and maximum likelihood mapping: exploring new tools for comparative genome analyses

Table 3 Summary of the genome quartets that include the mesophilic archaeon Halobacterium sp. or the thermophilic archaeon Archaeoglobus fulgidus, deep-branching bacteria Thermotoga maritima and Aquifex aeolicus, and bacteria Synechocystis sp. or Bacillus subtilis.

#	Genome 1	Genome 2	Genome 3	Genome 4	((1,2),3,4)			((1,3),2,4)			((1,4),2,3)
					Tot.	0.9	0.99	Tot.	0.9	0.99	Tot.	0.9	0.99
11	Synechocystis sp.	Thermotoga maritima	Aquifex aeolicus	Halobacterium sp.	29	20	12	45	34	27	86	69	56
13	Synechocystis sp.	Thermotoga maritima	Aquifex aeolicus	Archaeoglobus fulgidus	47	36	30	63	51	44	50	34	25
61	Bacillus subtilis	Thermotoga maritima	Aquifex aeolicus	Halobacterium sp.	44	32	27	27	19	11	83	62	53
62	Bacillus subtilis	Thermotoga maritima	Aquifex aeolicus	Archaeoglobus fulgidus	64	50	40	50	35	30	41	27	23

For table notations see legend for Table 2. Quartets #11 and 61 indicate that the majority of the QuartOPs group Halobacterium sp. together with Synechocystis sp. and with Bacillus subtilis respectively, which is in disagreement with 16S rRNA topology. In two control quartets (#13 and #62) Halobacterium was substituted with Archaeoglobus fulgidus, and in these cases the majority of QuartOPs support the topology that is in agreement with SSU rRNA topology.

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