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We also used a Bayesian approach that identifies the proportion of the posterior sample of viral topologies that match the host phylogeny (e.g. [ 19]).
It is notable that analysis of a relatively large and unbiased sample of viral sequences from multiple seasons with straightforward molecular evolutionary methods yields this unexpectedly complex picture of virus evolution.
To test for topological similarity, we compared the distribution of Robinson-Foulds [ 20] distance metrics provided by 10 random viral topologies to that derived from the posterior sample of viral topologies.
To increase sensitivity and obtain a small, representative sample of viral variants in a given population by Sanger sequencing, individual viruses can be isolated and amplified (biological clones) (Vignuzzi et al., 2005) or RT-PCR amplicons of the whole population can be subcloned into individual plasmids (molecular clones) (Levi et al., 2010; Sanjuán et al., 2010).
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A region approximately 1100 bases long was amplified from samples of viral DNA and fluorescently labeled with Cy5-modified dNTPs, and single-stranded DNA was prepared by strand separation.
Sampling of viral RNA molecules from an extraction solution that follows Poisson distribution is subjected to the stochastic effects of sampling variation.
In total, four samples of bacterial skin infections, two samples of viral skin infections, three samples of fungal skin infections and two samples of protozoic skin infections were investigated by HIF-1α-specific immunohistochemistry (Fig. 1).
In 1988, Shibata et al. [ 21] amplified 28 samples of viral isolates positive for CMV by PCR using IE and LA primers.
In addition, even better sampling of viral genomes may not allow explaining the presence of ORFans in some of the microbial genomes.
However, it is questionable whether a full sampling of viral genomes will provide homologs to 100% of the ORFans or only to a fraction of them.
Samples of viral RNA were obtained based on the extraction of total RNA from the plasma using the Total RNA Purification Kit NORGENN, Biotek Corporation, Canada).
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