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While this approach renders a quick way to prepare aligned samples, the extent of alignment is small for high-resolution structural studies on membrane proteins.
Most of these treatment methods work reasonably well when the proportion of gapped sites in an alignment is small [ 5, 6].
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In B, scaffolds encoding the loci are shown as horizontal gray bars (polymorphisms in the multi-sequence alignment are small vertical tic marks).
However, significant background MI can originate from random pairings of residues when the number of sequences in the multiple sequence alignments is small (in practice, less than 125 sequences [54]).
This is crucial for the applicability of the method, since the number of different columns in an alignment is really small compared to the dimension of these spaces.
The fact that the total tree length of the avian multiple species alignment is relatively small means that methods using just inter-species divergence to infer positive selection are expected to lack power [ 14].
The region of alignment of identical PBs is small (PBs k and l at the C terminal end).
The alignment of this HGC is small and very scattered.
The values of NA and NC show that Graemlin's alignment is far smaller than those from PINALOG, IsoRank and MI-GRAAL.
The simple two-species maximum-likelihood analysis based on the simulation data indicated that if the alignment blocks are small, the likelihood surface contour plot becomes broad (supplementary fig. S3, Supplementary Material online).
The value for k is small, so only a small number of alignments are discarded.
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