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All but one of duplicate alignments will be filtered to avoid redundancy caused by aligning once as individual reads and again as paired.
In these cases, alignments will be poor and phylogenetic analyses may be prone to long-branch attraction.
Clearly users who spend additional effort on improving the different aspects of the input alignments will be able to achieve higher detection rates.
Downstream inference methods that can explicitly cope with the inherent uncertainty in reconstructed alignments will be crucial for continued advances in comparative genomics.
Because of the shortness of the segments and their high divergence, HHpred E-values for many repeat alignments will be much higher than one would find acceptable in full-length protein/domain structure prediction.
Therefore, in cases where the optimal alignment score is distinctively smaller than any suboptimal alignment the kernel score including all suboptimal alignments will be close to the shortest-path approximation.
Similar(38)
Sometimes, regions at the beginning or end of the alignment will be poorly aligned because the sequences were too dissimilar in length.
If one strand contains a large chunk of DNA in reverse order, alignment will be thwarted.
In this sense, leveling and alignment will be more efficient.
More information about product availability and alignment will be available after that period.
When the problem instance is large, progressive alignment will be time consuming.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com