The substitution rate for each alignment column was divided by the codeml estimated alignment tree length to control for the mutation rate of the encoding gene.
The estimated alignment parameters of this process were finally applied to all other scans of each subject, to assure that the overall correction in brain size was the same for each subject, while the position was corrected individually.
YAHA next finds the best potential alignment in each region of the reference by combining the fragments that contribute to the highest estimated alignment score in that region.
The conservation scoring system relies on calculated "delta scores" – differences in estimated alignment scores between query and homologs, and query variants and homologs.
As a consequence, the estimated alignment length required for resolution of a region is small if one attaches more importance to the parametric simulation results (blue line) and much larger if one chooses to use the nonparametric simulation results (orange line).
Subsequently, the estimated alignment length required to resolve the region to that level of bootstrap support can be deduced by seeing where the dashed line crosses the line fitted through the data points and reading the corresponding value on the x-axis.
