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For each insertion branch in the comprehensive tree into which the candidate subtree shall be inserted, we once again conduct a case analysis to determine if the specific SPR move on the comprehensive tree also induces a change in the gene trees.
We obtain the per-gene insertion branch by recovering the two nodes that determine this branch via a recursive descent into the left and right subtree of the insertion branch in the comprehensive tree.
To achieve computational savings, we therefore use a simple linked list to store and look up the gene tree insertion branch nodes/likelihood score triplets.
The recursive lookups to search for gene nodes in the pruning branch and insertion branch subtrees are implemented naïvely, by recursive descents into subtrees.
If we consider the insertion branch, i.e. the branch of the comprehensive tree into which the subtree shall be inserted, we once again need to determine recursively, if the left or the right subtree of the insertion branch contains molecular data for a partition i (Fig. 5).
Case 1: if some nodes in the left and the right subtree of the insertion branch contain data for partition i as outlined in Figure 5, this means that the two subtrees must be connected by a branch of the partition, the partition insertion branch, into which the subtree shall be inserted.
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The statistical evaluation of SINE insertions was performed according to Waddell et al. (2001) where three insertions per branch are required to obtain significant support [ P = 0.037].
Branch diameter and branch insertion angle of both species are mainly related to branch cord length and relative branch position.
The monophyly of Pelecaniformes, Ciconiiformes, Procellariiformes, and Sphenisciformes was strongly indicated by the eight additional CR1 insertions found for branch 2 (P = 0.00015 [8 0 0]; fig. 3 B), suggesting the first divergence of Gaviiformes.
A fixed indel difference can be classified into one of four categories; 1) an insertion on the human branch, 2) a deletion on the human branch, 3) an insertion on the chimpanzee branch, and 4) a deletion on the chimpanzee branch.
To satisfy condition (3) the two branches for insertion or deletion are refined into four branches for regular or temporarily irregular insertion or deletion.
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