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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.

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

# 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
  1. 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.