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Because these differences are characterized by short branches, phylogenetic uncertainty was taken into account by setting branches to zero.
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In spite of the complicated Laplace inverse transform, we obtained an accurate and rapid solution by investigating appropriate branch points and poles and setting branch cuts.
Another performance split can be observed between pairs employing the same method for setting branch lengths but using MCC and TCB for selecting the topology.
For this purpose, we set branches connecting the multiple PDE1C genes of the stickleback as "foreground" branches.
A stramenopile clade is moderately supported (87% BS, 1.0 PP), and the only rhizarian (Bigelowiella natans) in our data set branches separately.
The set of network equations are formed by equating the loop currents to the algebraic sum of the tie set branch currents.
The set of network equations are formed by equating the node pair voltages to the algebraic sum of the cut set branch voltages.
We assembled a composite phylogeny for the taxa included in the EPCA using published studies of rattlesnake systematics [ 19- 22] (Fig. 2), and set branch lengths equal to one.
We ran branch-site tests for each group by setting all branches within each group in turn as foreground branches.
Despite the optimal setting, branching of the tree is still considerable.
The branch-site model A1 in combination with the BEB procedure was specified by setting the branch of A. ilicifolius as the "foreground branch" and all other branches in the tree as "background" branches.
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