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This also explains the absence of a bootstrap support for a monophyletic clade of I. canariensis ITS sequences because of long branch problems due to accelerated rate of substitution and more certainly to recombination.
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It is also shown in this paper that the "false branch" problem can be overcome by the importance sampling technique.
Traditional second-order RSM without cross terms may be inaccurate and may suffer from the problem of low convergence rate and the second-order RSM with cross terms may encounter the "false branch" problem.
The saturation phenomenon is part of the long branch problem.
Long-branch attraction does not require convergence of the sequences (Felsenstein 1978), but the over utilization of only a subset of codons may exacerbate the long branch problem by superimposing convergence on the long branch problem.
This avoids the need to assemble the mechanism in the initial position (and associated branching problems), gives more uniform spanning of the solution space, and guarantees that at least the starting configuration for the ODEs IVP exists and is known.
This method allows to find automatically all the components of a complex object in which branching problems may occur and to determine how they are linked together.
The other major advantages of this method are to perform segmentation and surface tracking simultaneously, to describe complex structures in which branching problems can occur if the segmentation is purely local, and to provide accurate and reliable results.
Although we tried to break down long branches by a dense taxon sampling, some long-branch problems persisted.
Previous conflicting reports that show Polypodium and myxozoans form a sister taxon to Bilateria [ 2- 4] can be explained by limited taxon sampling and an inadequate number of informative characters in their analyses, both of which confound long-branch problems.
But there is no reason why some other proteins should not have similar long-branch problems, as many paralogues are deeply divergent and thus have a highly stretched stem on paralogue trees.
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