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Qualitatively, results were unaffected by whether alignment gaps were or were not included in the analysis.
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Our experiments with PHOG-BLAST showed that the correlation coefficient threshold r* that determines whether an alignment column should belong to a cluster is 0.5.
This was done to investigate whether alignment-dependent biases (Löytynoja and Goldman 2008) influenced our results.
These datasets allow us to test whether alignment-free methods are able to discriminate in vivo identified enhancers that show similar activity from genomic background.
We summarize whether alignments supporting the SV are better than both of the alignments supporting contiguous fragments with a probability-based score.
The test of whether alignments of restriction digest optical maps supported the presence of evolutionary strata in M. lychnidis-dioicae provided a negative but nonconclusive result.
Alignment tools typically report their output in the standard SAM (Li et al., 2009a) file format, which defines a mapping quality field that aligners can use to signify whether an alignment is likely to be correct.
Upon closer inspection, the results of our experiment indicate a significant degree of disagreement between the respective scores: only in 28% of the 2500 pivot-versus-counterpart alignments, all three scores agree on whether the alignment produced by DALI or by TM-Align is the best.
It is unclear whether postural alignment is a significant risk factor.
These results may provide quantitative information that can be used to assess whether dust alignment in planetary formation region is caused by a simple Langevin process or not.
This study seeks to assess whether political alignment of a provider's county is associated with provider attitudes and behaviors regarding EC.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com