ancestral: Accept files to `--genes` #1873

Job	Run time
pathogen-repo-ci (avian-flu)	41s
test (python=3.8 biopython=1.76)	6m 59s
pathogen-repo-ci (ebola)	55s
test (python=3.8 biopython=1.79)	6m 50s
pathogen-repo-ci (lassa)	56s
test (python=3.8 biopython=1.80)	6m 35s
pathogen-repo-ci (mumps)	59s
test (python=3.8 biopython=latest)	6m 59s
test (python=3.9 biopython=1.79)	6m 44s
pathogen-repo-ci (ncov)	1m 12s
test (python=3.9 biopython=1.80)	6m 42s
pathogen-repo-ci (rsv)	2m 51s
test (python=3.9 biopython=latest)	6m 41s
pathogen-repo-ci (seasonal-flu)	1m 1s
test (python=3.10 biopython=1.80)	6m 43s
pathogen-repo-ci (tb)	1m 19s
pathogen-repo-ci (zika)	51s
test (python=3.10 biopython=latest)	6m 43s
test (python=3.11 biopython=1.80)	6m 56s
test (python=3.11 biopython=latest)	6m 55s
build-docs / build-conda	0s
build-docs / build-pip	50s
codecov	20s
	1h 26m 42s

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