Genomic and transcriptomic data analyzed in this study is available at NCBI SRA (PRJNA36679; PRJNA36679).
DOI: http://dx.doi.org/10.7554/eLife.05055.020 The genomic and epidemiological data analyzed here provide important insights into the phylodynamics of the two lineages of influenza B virus currently circulating in humans.
Genomic data were analyzed using Perl scripts specifically written for this study (available at http://treenome.tamu.edu/).tamu.edu/
The genomic data were analyzed using two different methods.
Seed contigs from de novo assemblies of all genomic data were analyzed for high coverage and for the presence of common mitochondrial genes.
To determine the phylogenetic position of Chlorokybus as inferred from mitochondrial genomic data, we analyzed an amino acid data set containing a total of 4,024 sites using the ML method.
For researchers, knowledge of the contextual features of this 'original' trust relationship between research participants and the research team – such as for example, the person who obtained consent - was essential in ensuring that genomic data were analyzed appropriately.
As noted above, there are two typical approaches to using genomic data for analyzing protein function: methods that directly associate proteins with particular processes or functional classes, and methods that focus on predicting functional associations or interactions between pairs of proteins.
An important advantage of the GOS dataset is that genomic data can be analyzed in relation to the location at which the samples were obtained.
This genomic data was then analyzed using GenePattern [ 17].
