The other examples show some other cases in which the alignment makes the difference between the hypotheses.
When the theoretical sessions continued, students used the acquired images to learn about data reduction and image processing, procedures and benefits of image stacking and alignment, and the difference between properties such as contrast and brightness.
A formal way to quantify the effect of stochastic sampling is to perform a Shimodaira-Hasegawa permutation test on columns of an alignment, compute the difference in log-likelihood scores of two competing models on each replicate (if they have the same number of parameters), and test the hypothesis that the difference is different from zero.
We observed that the sequential removal of rapidly evolving categories of sites from the alignment decreased the difference, in terms of nodal distance RMSD, between the phylogeny produced and the ideal phylogeny.
Positions in the alignment where the difference in means (psychrophile proteins – mesophile proteins) between the two groups exceeded the sum of the standard deviations were flagged as sites of significant deviation.
In this case, with the same evolutional distance and console length, the accuracy and confidence values of the global alignment are somewhat higher than those of the local alignment, this difference increasing with the growth of the evolutional distance.
We eliminated alignments where the difference in amino acid identity between the most-similar and least-similar pairs of species were greater than 60% out of concern that these might not be true orthologs.
Reads with multiple alignments are more likely to be aligned to different locations by different aligners, due to the difference in alignment strategies these aligners employ, as well as the standards of how to randomly choose one alignment to report.
For the leveled-type alignment scenario, the differences between wires were up to 70 g (range 110 to 179 g).
When using high-quality raw data and liberal alignment criteria, the differences between the tools were relatively small.
