fix: explicitly specify how the root and ambiguous states are handled… #3049

Job	Run time
check-docs	35s
mypy	49s
pathogen-repo-ci (dengue)	2m 44s
pathogen-repo-ci (lassa)	41s
pathogen-repo-ci-v0 (avian-flu)	51s
pyright	20s
pathogen-repo-ci (measles)	1m 21s
pathogen-repo-ci-v0 (ebola)	53s
pathogen-repo-ci (mpox)	1m 14s
pathogen-repo-ci-v0 (mumps)	54s
test (python=3.8 biopython=1.80)	11m 35s
pathogen-repo-ci (seasonal-cov)	1m 48s
pathogen-repo-ci-v0 (ncov)	1m 11s
pathogen-repo-ci (zika)	1m 7s
test (python=3.8 biopython=1.82)	11m 42s
pathogen-repo-ci-v0 (rsv)	8m 24s
test (python=3.8 biopython=latest)	11m 43s
pathogen-repo-ci-v0 (seasonal-flu)	1m 20s
test (python=3.9 biopython=1.80)	11m 52s
pathogen-repo-ci-v0 (tb)	1m 17s
test (python=3.9 biopython=1.82)	11m 52s
test (python=3.9 biopython=latest)	11m 52s
test (python=3.10 biopython=1.80)	11m 57s
test (python=3.10 biopython=1.82)	11m 52s
test (python=3.10 biopython=latest)	11m 52s
test (python=3.11 biopython=1.80)	11m 51s
test (python=3.11 biopython=1.82)	11m 54s
test (python=3.11 biopython=latest)	11m 51s
test (python=3.12 biopython=1.82)	11m 52s
test (python=3.12 biopython=latest)	11m 52s
build-docs / build	2m 15s
release	0s
codecov	0s
rebuild-docker-image	0s
	3h 13m 21s

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