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To evaluate the effect of varying alignment parameter values on cladogram topology, independent analyses of the complete data set were performed for a range of parameter combinations (sensitivity analysis sensu [ 103]) under parsimony.
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The most commonly used aligners have varying alignment quality and speed, tend to depend on a specific reference alignment, or lack a complete description of the underlying algorithm.
Accuracy was used as measurement for the proportion of true classifications by DeconSeq and calculated for thresholds of 95% query coverage and varying alignment identity.
The accuracy values were calculated for threshold values of 95% query coverage and varying alignment identity.
Securing these types of legitimacy is shown to require the adoption and alignment of varying legitimation strategies according to the constituency practitioners seek to influence.
To obtain such estimate, the alignment was repeatedly randomly sampled to create smaller alignments of varying size, whose entropy was measured.
Kinjo and Nishikawa[9] analyzed a set of amino acid substitution matrices constructed from multiple alignments of protein families of varying percent sequence identities (%ID).
The terminal portions of the alignment could, therefore, simply be assumed to be gapless while the linkers of varying lengths between the termini and the globular structure (current alignment) can be more or less ignored.
One advantage of such a method consists mainly in avoiding the alignment step, and can be used on numerous sequences of varying size.
HMGB-UBF HMG-domain sequences contained a small section of varying size within the core region that was removed to create a compact alignment with conserved sections only.
Alignment of the rbcL– psaI region from each Poaceae taxon revealed that differences in annotation result from deletions of varying size.
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