Sentence examples for calculated using the alignment from inspiring English sources

Sequence divergence was calculated using the alignment region with sequence in all species compared.

To find the confidence interval around a reference tree, the site-wise log likelihoods were calculated using the alignment for the reference tree.

Alternative alignments and trees were calculated using the alignment programs ClustalW [ 42] and T-Coffee [ 43], and the neighbour joining (PHYLIP package 3.66 [ 44]; distances calculated using ProtDist [ 45] or MRBAYES (v3.1.2, [ 46] phylogeny programs.

Nucleotide substitutions levels were calculated using the alignment of MYB domain of GmMYB proteins by Hyphy version 2.0 [ 80] along with a corresponding NJ phylogenetic tree (Additional file 6).

Finally, the average identities and coverage were calculated using the alignments for each primate species (Table  3).

The input for mothur is the distance matrix we calculated using the pairwise alignment instead of the default multiple alignment.

The percent identities for the coding and intergenic regions and the non-edited proteins were calculated using the GLOBAL alignment feature in BioEdit 5.0.9 by pairwise comparisons of the three clades (Table 2).

Distances were calculated using the concatenated alignment of 63,987 informative SNPs that estimates the diversity between S. Schwarzendgrund, S. Javiana, S. Pomona and the major clades of S. Montevideo observed.

The nucleotide probabilities for each state were calculated using the predicted gRNA alignments generated by local alignments (Fig 7).

The average sequencing depth and coverage was calculated using the results of alignment.

The identity of the amino acid sequences of the orthologous V1Rs was calculated using the EMBOSS pairwise alignment algorithms [ 50].