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A formalism to analyze divergence at two fold redundant codon systems is presented.
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We achieve this by analyzing divergence times of sequences using a strict phylogenetic approach, as opposed to divergence times of species using a phylogenetic-coalescent approach [ 19].
More recently Santini et al. [ 96] analyzed divergence times for major fish lineages including those of Otophysi to investigate the effects of fish-specific whole-genome duplication events on the radiations of teleost fishes.
With this calibration point, substantial over-dispersion was observed for all analyzed divergence time estimates, so these results are likely to be a branch-length-related artifact (see above).
Therefore, protein 3D structure comparison becomes an important tool to analyze structural divergence and in turn functional divergence.
In this paper, a convenient method to analyze the divergence performance of a collimating system is presented.
As a first test for the relevance of these findings to transcriptional regulation, we used a novel paradigm to analyze the divergence in putative transcription factor binding sites in HARs nearby genes in our microarray study.
> > -wrap-foot> There are several ad hoc distance measures that have been used to analyze the divergence in expression.
The predicted coding sequence for each reftig was then used to analyze sequence divergence from C. gigas.
CLC Sequence Viewer was used to construct phylograms for both proteins from the MSA obtained from BioEdit, in order to analyze the divergence among the retrieved sequences.
Moreover, we evaluate the usefulness of the 18S gene for phylogenetic inferences by combining our new authentic solenogaster 18S data with published molluscan sequences and - based on an extended taxon sampling - analyze sequence divergence and compositional heterogeneity within the phylum.
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