We lowered the stringency (identity degree) from 90% to 80% in consideration of genomic divergence.
However we show that consideration of sequence divergence is critical for correct prediction in certain cases and can sometimes flag non-cleaved or misannotated targeting signals.
ML estimates the probability of ancestral states given a model of evolution and takes into consideration the age of divergence between clades.
Based on their close relatedness it has been proposed that the two species should be reclassified as a single one, a proposition that was subsequently rejected in consideration of their extreme divergence in pathogenicity, life cycle and public health impact [20], [21].
Survey results and consideration of convergence and divergence were integrated into the manuscript and the final draft was sent to the developers/experts for final approval of accuracy.
Divergence of visions of the future is, as briefly mentioned above, the result of the consideration of controversial and divergent knowledge bases and disputed values during their creation: the divergence of futures mirrors the differences of contemporary positions and reflects today's pluralism.
Taking this into consideration, a divergence time of ∼180 Ma was calculated for two species of Ciona (Berná et al. 2009).
This highlights the importance of assessing proposed vicariant patterns with a careful consideration of phylogeny, geology, and estimated divergence times [ 22].
We did not include mouse lemur, a primate which diverged earlier from human, in our analysis due to lower genome quality and divergence time consideration of its genome.
It is also intuitive that percent alignment length would be positively correlated with the D. yakuba vs. D. melanogaster hybridization ratio, as it is another measure of divergence that is not taken into consideration by %ID.
This model allows independent consideration of the effect of 'Clade' (clade divergence) and 'Stx' (stx type variation) parameters on differences in gene expression among O157 H7 strains, as well as their interaction (combined) effect (Clade:Stx).
