Figure 2.

The pseudo-likelihood of a four-taxon species tree. a) The rooted triples of a four-taxon species tree. There are four rooted triples in the four-taxon species tree. The lengths of two internal branches in the species tree are T1 and T2. The lengths of internal branches in the four triples are B1=T1, B2=T1+ T2, and B3=B4=T2. b) The pseudo-likelihood of a four-taxon species tree. The species tree (bold lines) has two internal branches with lengths of T1 and T2. The dataset contains three gene trees (thin lines). Different gene tree triples correspond to different species tree triples. For example, triple ab|c in gene tree 1, ac|b in gene tree 2, and ab|c in gene tree 3 correspond to triple AB|C with internal branch length B1 = T1 in the species tree, while triple cd|a in gene tree 1, ac|d in gene tree 2, and ac|d in gene tree 3 correspond to triple CD|A with internal branch length B2 = T2 in the species tree.

Liu et al. BMC Evolutionary Biology 2010 10:302   doi:10.1186/1471-2148-10-302
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