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It is to be noted that unlike the case of the 1D Py/Fe nanostripe array of[7], no interfacial air gaps were considered in the calculations, as the fabrication process employed here precludes their formation.
Gaps were considered missing.
Pairwise or complete deletion of gap positions does not yield significant differences in the results because of the small amount of gaps in the MSA (only positions with less than 2% gaps were considered).
Gaps were considered a fifth state [ 65].
Gaps were considered as missing data.
No positions containing gaps were considered in the phylogeny analysis.
Similar(38)
The effects of various parameters on the gaps are considered.
Gaps are considered for each site independently.
Therefore, amino acid sites with alignment gaps are considered as positively selected if they are identified by the population genetics approach with a posterior probability higher than 95%.
Because gaps are considered as missing characters, we have not taken codons with deletion into account in our statistics using ancestral genomes.
We adopted this treatment of gap characters so that the divergence of orthoMSA columns with many gaps is considered high (we also tried using straight entropy, but the results, not shown, were slightly worse).
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