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aThese values are likely considerably erroneous due to the crossing of bands in some alignments confusing the averaging of VS and ILS, and the vast effect alignment has at this low separation.
In the present study I used several simulations to assess how various permutations of the alignment algorithm effect alignment quality and speed.
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However, there could be long-branch effects or alignment effects for the NP phylogeny as the exclusion of the distantly related Morbillivirus sequences yielded the same mammalian paraphyly, but increased the support values (Fig. 4).
Greater than 54 % of reads mapped to the reference allele at heterozygous sites in both BWA alignments (Table 1), demonstrating the effect of alignment bias on non-allele-aware alignments.
Using region specific template sequences had no significant effect on alignment quality but increased the pairwise alignment speed by up to 116% (Table S4).
To isolate the effect of alignment we applied a linear SVM to the alignment model determined by the HMM.
Figure 5 demonstrates the effect of alignment in the case of using 2-nonanone for alignment of an analysis of the 15-analyte mixture (see Table 1).
In order to determine the effect of alignment gaps, we also analyzed our sequences with the 66 alignment gaps included and treated them as ambiguity data [ 42, 43].
To assess the effect of alignment error in the RA, the sequences were re-aligned with PAGAN and MAFFT (Katoh et al., 2002).
The length of the sequences had less effect on alignment quality, although longer sequences tended to be less well aligned.
Quantitative assays are needed to determine the effect of alignment on contractile function and muscle physiology.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com