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Ideally the difference measure should detect divergence within one base and account for small differences in the curve to allow the detection of convergence within 2 4 bases.
There are a growing number of examples of morphological divergence between subspecies in which researchers have been unable to detect divergence in a variety of selectively neutral loci [13].
Unfortunately, we were unable to obtain ndhF sequence from A. tenella, thus limiting our ability to detect divergence.
In short, the biology of HBV may limit both the presence of and the power to detect divergence points.
Thus, it appears that the power of this method to detect divergence points may falter near the boundary of biological relevance.
In the next section, additional simulations investigate the amount of information, as measured by the sequence divergence, alignment length, and number of taxa, needed to detect divergence points.
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An alignment of 134 RIFIN protein sequences from the P. falciparum reference strain 3D7 (selection criteria detailed in Methods) was analyzed in order to detect divergences within the family.
Thus, detecting divergence in closely related or recently diverged species phylogenetically can be difficult if monophyly has not been reached.
Comparing the curves requires quickly detecting divergence and smoothing over small differences to locate convergence points.
Gu [ 36] describes a maximum likelihood method for detecting divergence points associated with gene duplication.
Analyzing fragment data assuming a stepwise mutation model or complete independence of repeats can cause problems in detected divergence.
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