Hi everyone
I’m a bit new to phylogenetics. I would like to know how nextstrain samples available influenza sequences to ensure that the sequences used to construct the tree are representative of all areas of the globe.
Welcome, @why_man500! The seasonal influenza builds are produced using the code at https://github.com/nextstrain/seasonal-influenza.
Subsampling happens in this workflow step, using a custom select_strains.py program.