To this end we first construct substitution matrices from pairwise protein alignments with a degree of sequence identity varying from 99 down to ten percent (corresponding to degrees of divergence between one and 90 percent) in steps of one percent and correlate them with the matrix of differences in volume, hydrophobicity, polarity and average codon sequence difference.
The sequences of every cluster were aligned using mafft (Katoh and Standley, 2013), and the cluster 'radius' was computed as the average of the percent divergences of every sequence pairs in the cluster.
The means of percent divergence for each lineage were used as thresholds.
As expected the ancestral AluY subfamily (orange) showed the broadest distribution of percent divergence from the AluY consensus sequence.
The distribution of percent divergence from each subfamily consensus sequence is shown in figure 2. A total of 30 elements (N = 26 Ya5, N = 3 Yb9, and N = 1 Yb8) were scored by RepeatMasker (Smit et al. 1996 2010) as having 0.0% divergence from their respective consensus sequences (about 9.3% of the data set).
The average half-life of insertions in invertebrates, 1.4 (0.3) in units of percent sequence divergence among paired LTR sequences, is significantly lower than that for pre-KT mammals and land plants, 5.3 (0.5) and 4.4 (0.9), respectively, although perhaps not much lower on a per-generation basis.
A summary of this data is presented in Additional file 3. Since mutation saturation can also occur in cyt- b when synonymous substitutions occur in the third codon position, we plotted pairwise comparisons of overall percent sequence divergence versus number of substitutions.
Two measures of the power of a locus to discriminate among species were calculated: 1) percent sequence divergence between pairs of species and 2) the proportion of the 48 genera for which species in a pair could be differentiated.
For all alignments, PAUP* was used to determine percent sequence divergence, number of parsimony informative characters, and concordance with the Rickettsia species tree.
To estimate the percent divergence of dengue type 3 viruses, a distance matrix of nucleotide and amino acid sequences, based on the 1023 nucleotides of E gene, was constructed (Table 1).
