Merge pull request #1751 from nextstrain/james/refine-prune-outgroup #3327

Job	Run time
test (python=3.9 biopython=1.80)	14m 24s
test (python=3.9 biopython=1.82)	13m 42s
check-docs	39s
mypy	54s
test (python=3.9 biopython=latest)	13m 55s
pathogen-repo-ci (dengue)	3m 24s
pathogen-repo-ci (lassa)	8m 14s
test (python=3.10 biopython=1.80)	14m 48s
pathogen-repo-ci-v0 (avian-flu)	1m 27s
pyright	11s
pathogen-repo-ci-v0 (ebola)	1m 26s
pathogen-repo-ci (measles)	1m 53s
test (python=3.10 biopython=1.82)	14m 7s
test (python=3.10 biopython=latest)	14m 30s
pathogen-repo-ci-v0 (mumps)	1m 33s
pathogen-repo-ci (mpox)	1m 49s
test (python=3.11 biopython=1.80)	14m 29s
pathogen-repo-ci (oropouche)	1m 53s
pathogen-repo-ci-v0 (ncov)	1m 36s
test (python=3.11 biopython=1.82)	14m 36s
pathogen-repo-ci (rabies)	3m 3s
pathogen-repo-ci-v0 (rsv)	9m 16s
test (python=3.11 biopython=latest)	14m 21s
pathogen-repo-ci (seasonal-cov)	2m 23s
pathogen-repo-ci-v0 (seasonal-flu)	1m 54s
pathogen-repo-ci (wnv)	1m 43s
test (python=3.12 biopython=1.82)	21m 48s
pathogen-repo-ci-v0 (tb)	1m 58s
pathogen-repo-ci (yellow-fever)	4m 47s
test (python=3.12 biopython=latest)	22m 33s
pathogen-repo-ci (zika)	1m 45s
build-docs / build	2m 11s
codecov	11s
release	0s
rebuild-docker-image	0s
	3h 47m 23s

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