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Phylogenetic and divergence considerations suggest that a 544-bp fragment of rps3 was transferred to the nuclear genome shortly after divergence of the A- and D- genome diploid cottons.
The 3 patients with primary bacteraemia due to Granulicatella spp. with intermediate susceptibility or resistance to penicillin were successfully treated (cases 7, 10 and 11). A. defectiva and Granulicatella spp. are now considered as two distinct genera based on 16S rRNA tree topology and sequence divergence considerations [ 7].
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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.
On the other hand, the Syn score takes the full divergence information into consideration, approaching high values only when two trees are highly similar.
Divergence range takes into consideration the road functional classification [12], meaning that overcoming this divergence points out to change of road functional category.
To this purpose, a second method has been taken into consideration: the divergence measure called Kullback-Leibler divergence, that is defined as D KL ( P ∥ Q ) = ∑ i P ( i ) log P ( i ) Q ( i ), (4).
Taking this into consideration, a divergence time of ∼180 Ma was calculated for two species of Ciona (Berná et al. 2009).
The difference in the percent mapping between the species partially reflects the difference in the sizes of the databases and the phylogenetic divergence among species under consideration (Additional file 3: Figure S2).
Aside from reverse causality and confounding, which are certainly important considerations, such early divergence in the survival curves can also be explained by two other factors.
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.
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