Sentence examples for alignment excluding from inspiring English sources
Because the hypervariable regions would potentially mask phylogenetic signals due to extensive homoplasy [65], we opted for performing subsequent analyses on the complete ITS dataset (from here on referred to as full dataset), as well as on the ITS alignment excluding the hypervariable regions (from here on referred to as stripped dataset).
Whether the cyanobacterial alignment (excluding the outgroup) was substitutionally saturated was tested using the program DAMBE [ 109, 110].
Overall identity is the number of matching residues, divided by length of the alignment excluding possible introns.
Base composition was computed for all taxa on the concatenated alignment excluding constant sites to gauge the effect of possible base compositional bias on the resulting phylogeny.
A multiple alignment excluding the ~35 aa segment of HrgC proteins was also generated with aLRT (alternative likelihood ratio test) values.
c Percent similarity reflects the number of nucleotide matches over the total length of the alignment, excluding the third base of the anticodon triplet.
Initial sequence alignments were generated using MUSCLE v3.8.31 (Edgar 2004), with some adjustments made by eye and regions of uncertain alignment excluded using Se-Al 2.0 (Rambaut 2008).
Thus, some fraction of insert-adapter-chimeras or pure adapter dimers may end up in the final data analysis; where they may cause false alignments or, due to unsuccessful alignment, exclude short-insert-size molecules from analysis.
A sliding window analysis of polymorphism and divergence was calculated with DnaSP using 36 S. cerevisiae strains and 1 S. paradoxus strain, CBS432, with gaps in the alignment excluded.
Following this assessment, datasets were concatenated for myzostomids and crinoids to include (where applicable) COI and CytB with third codon removed, and, 16S, 18S, 28S, and H3 with ambiguous areas of the alignment excluded, as determined by GBlocks.
The length of the individual and trimmed alignments excluding gaps varied from 126 to 1167 nt, with an average of 505 nt (Figure 1).
