Although this may appear to agree with the fact that functional assays suggest that both variants are at least partially functionally comprised, it should be noted that the posterior probabilities were driven by the sequence alignment component of the analysis.
I suggest that De Waal's approach could benefit from a more thorough alignment with the analysis of the workings of sympathy in the work of Darwin and Adam Smith.
XL and SL carried out the sequence alignment and the analysis of the correlation of sequencing errors between two platforms/samples.
Since a proper alignment of the molecules prior the analysis is crucial to the successful application of these models in further studies, the molecules were aligned based on their pharmacophore features.
Figure 5 demonstrates the effect of alignment in the case of using 2-nonanone for alignment of an analysis of the 15-analyte mixture (see Table 1).
To this end we analysed in detail the scores obtained with different combinations of program, query alignments, and COACH reference alignments (the analysis of any such combination will be referred to as a "run" below).
A PHYLIP processing of all ClustalW alignments allowed the analysis of the Jmjd6 phylogeny in relationship to all other identified DSBH domain containing proteins.
Because the possibility of multiple insertions and deletions prevented an exact alignment of the nontranslated sequence, phylogenetic analysis was conducted with only the protein-encoding sequence.
In the resulting pHMM alignment, the analysis of characteristic sites was performed as described above.
Future approaches should try to minimize the effect of alignment quality on the analysis results.
