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Bertolino and Gnesi (2003) propose a template called PLUC Product Line Use Casess) that allow variations to be described, by explicitly enclosing within the sections of the use cases some tags that indicate the variable parts.
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The most commonly used methods rely on codon substitution models that allow variation in the intensity of selection among codon sites within a gene [ 42, 43].
Here we estimated selective pressure on rbcL using different types of Markov models of codon evolution: (1) site-specific codon models that allow variation of selective pressure among sites in a sequence, and (2) switching codon models that allow variation of selective pressure among sites and over the evolutionary time.
In order to test specifically for this hypothesis while controlling for contribution of a relaxation of selective constraints, we performed another codeml analysis that compares two different models that allow variation of ω values between codons.
The extrapolation chamber is a parallel-plate ionization chamber that allows variation of its air-cavity volume.
This conjecture was supported via interview data, wherein students reported that they used the feature that allowed variation in both graphs for checking how representations were related.
The model class is implemented in a visualization tool that allows variation of the model parameters and visualization of the resulting model for the given set of parameters.
In addition, we also determined the sites evolving under positive selection in a specific clade with the branch-site model that allows variation in ω across individual codons on a specific lineage [ 27].
However, we still see a number of proteins in any genomic subset with a substantial number of unique epitopes (even by the relaxed JanusMatrix evaluation that allows variation in the MHC-facing residues).
Early investigations indicated that allowing variation in both date of birth and event dates leads to an unacceptable number of erroneous matches.
For this reason, a branch-sites method has been developed that allows variation in ω across individual codons on a specific lineage [ 46, 58].
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