Add frequencies plot

[j23414]

Context

As part of broader issue to add frequency panels to pathogen pipelines nextstrain/public#6

A frequencies plot provides a dynamic representation of how genetic variants or clades change over time. This visual aid helps researchers and public health officials to:

• Track the rise and fall of specific mutations or lineages
• Identify emerging trends in pathogen evolution
• Observe seasonal patterns or other temporal dynamics

Specifically to WNV, determine if a frequencies plot of pathoplexus global lineages (perhaps yes) or USA-based lineages (perhaps not...) would be useful. The decision of lineage naming conventions can be different for the global vs state-based sites.

Description

Add a frequencies panel to the WNV trees using augur frequencies. A key note is that the tip IDs must match the tip IDs on the auspice tree so be careful if there are any set_final_strain_name.py code. This naming will be a potential complication for segmented viruses (not WNV).

Examples

Follow pattern from dengue, yellow-fever and measles pipelines.

Possible solution

(Optional)