SARS-CoV-2 double annotation causes confusing annotation changes

[lilymaryam]

Putting annotated MATs through autolin is relatively straightforward (I will make a pipeline to increase ease for users), however, the annotated SARS-CoV-2 phylogeny provides additional challenges due to the use of both nextstrain and pango annotations on each node of the pb. I will need to create specific flags or commands for SARS-CoV-2 to avoid certain confusing outputs I have observed. For the alpha release, users should use the SARS-CoV-2 MAT with additional caution.

[lilymaryam]

The last comment still stands; however, I have created a SARS-CoV-2 example subtree that avoids the dual annotation issue, so it may be safely used for examples. The larger issue is still to be addressed.