Add subclade variant classification - #44
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Description of proposed changes
Adds another variant classification to the workflow to calculate frequencies and fitnesses for named subclades without any finer-grain amino acid classification. Our current frequency visualizations for emerging haplotypes show ancestral subclade frequencies as exclusive of the derived subclade frequencies. These visualizations could give viewers the false impression that the ancestral subclade is declining in frequency when it has really become so successful that its descendant subclades have started to grow, too. The coarser view given by this PR's changes allows users to see the "inclusive" frequencies for each named subclade.
The following are example H3N2 regional subclade frequencies and fitnesses:
And H1N1pdm regional subclades:
Related issue(s)
Closes #31
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