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Moreover, we found that LD patterns can be useful in distinguishing the patterns predicted by different evolutionary models.
A direct comparison between energy values obtained by different evolutionary models emphasizes a good and competitive performance of the proposed method.
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These evolutionary scenarios can be evaluated by applying different evolutionary models of character change in a phylogenetic framework [ 19].
Other studies have traced the evolution of introns across the major eukaryotic lineages by using different evolutionary models [ 22, 23].
Sequences were aligned using ClustalX Maximum likelihood estimates of dN/dS (the parameter) for each lineage in the phylogenies (see Figure 3) were derived by a method employing different evolutionary models, using the CODEML program of PAML Version 3.0 b [ 14, 15, 40, 41].
The output from TranAlign was converted to Nexus/PAUP format and submitted to the software program ModelTest [ 60] for selection of the most appropriate model of evolution for each dataset by testing the fit of 56 different evolutionary models with the data set.
We used a posterior predictive approach to determine whether the observed MDI differed from the various evolutionary expectations of the different evolutionary models [ 39].
This allowed us to explore different evolutionary models addressing the technical systems used in the area.
Four different evolutionary models were used for each seed sequence (JTT, WAG, Blosum62 and VT).
To compare the evolutionary rates obtained using different evolutionary models and methods we assembled four small representative sets of aligned cCP sequences.
For a given phylogeny, the likelihoods of different evolutionary models can be compared using assigned or estimated ω parameters.
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