We build a hierarchical tree using complete linkage (furthest neighbor) agglomerative clustering, based on pairwise identity distance (100%% − identity %).
The examples given in Table 1 illustrate that the metric featured by DBC454 is, for example, less sensitive to this type of errors than a metric based on pairwise sequence identity.
For copies lacking one or two LTRs (i.e., truncated copies of LTR retrotransposons or copies of other types of TEs such as LINEs or DNA transposons), the method currently used is based on pairwise nucleotide identity between elements that are closely related at the phylogenetic level or between genomic copies and a consensus of the element [ 36- 38].
Clustering all our P450s genes was also performed based on pairwise sequence percentage identity using the complete linkage algorithm [ 12].
Based on pairwise alignments, amino acid identity was calculated for homologous genes.
Based on pairwise structural alignment, the amino-acid sequence identity between MmNQO and SmMdaB is 23.5%, whereas the identity is only 16.5% between SmMdaB and EcMdaB, revealing a more distant relationship between the two MdaBs.
Sequence identity is measured based on pairwise realignment to the human sequence.
The identity distribution chart is plotted based on pairwise alignments computed between all members of the selected virus family or group.
A putative autonomous representative (HeligloriaAi) was found in six different insect species (D. yakuba, D. ananassae, D. willistoni, A. pisum, R. prolixus, and B. mori) with levels of sequence identity ≥90% (over 768 3,927 bp) based on pairwise comparisons of the internal region (see supplementary Dataset S1, table S3.1, fig 1 b, Supplementary Material online).
As described in the previous section, we tracked the identities of the modules across all runs based on pairwise module distances, and thus characterized the stability of the modules.
