clades: Match via 'alleles' rather than 'mutations'
clades: Match via 'alleles' rather than 'mutations'

Store and match clades and mutations as a triple of gene / site / alt or HA1 / 159 / Y. Depending on tree density there may be different sets of mutations, but the resulting alleles should remain consistent.
nextstrain/augur,nextstrain/augur,blab/nextstrain-augur,nextstrain/augur