Fine tune the "Dengue virus DENVx genotypes" dataset

[j23414]

Dengue virus DENVx genotypes

An update regarding the classification of dengue virus (DENV) genotypes. As suggested by @rneher in a Slack channel, adding an outgroup seems to have mostly resolved the issues with cross-serotype false positives for DENV1, DENV3, and DENV4 genotype classifications.

DENV1, DENV3, and DENV4 Genotype Classifications

The following images show the improved genotype classifications for DENV1, DENV3, and DENV4 after incorporating the outgroup:

The green color indicates within-serotype classifications, which is a positive outcome.

DENV2 Genotype Classification

However, the DENV2 genotype classification still requires further improvement:

The reconstructed "all" root was too similar to a DENV2 genotype, so it has been swapped with DENV4.

Next Steps for DENV2

The current plan is to add the reconstructed roots of DENV1, DENV3, and DENV4 as outgroups to DENV2 to further enhance the genotype classification accuracy across all serotypes. Although please feel free to submit other suggestions.

[j23414]

I had to regenerate the denv2 tree a few times with the new outgroups, but this one seems to be working.