Adds logic to the early H3N2 HA workflow to generate embeddings from observed and ancestral sequences and include these embeddings alongside the original embeddings based on observed sequences only. Updates the Auspice config JSON for early H3N2 HA, too, to include these ancestral embeddings. This commit paves the way for plotting of branches between samples in the embeddings by producing an "annotated embeddings" table with embedding coordinates for both internal nodes and tips.
huddlej
commented
9 months ago
Adds logic to the early H3N2 HA workflow to generate embeddings from observed and ancestral sequences and include these embeddings alongside the original embeddings based on observed sequences only. Updates the Auspice config JSON for early H3N2 HA, too, to include these ancestral embeddings. This commit paves the way for plotting of branches between samples in the embeddings by producing an "annotated embeddings" table with embedding coordinates for both internal nodes and tips.
Related to #50