ancestral: Accept files to `--genes` #1909

Job	Run time
pathogen-repo-ci (avian-flu)	43s
test (python=3.8 biopython=1.76)	7m 33s
pathogen-repo-ci (ebola)	1m 1s
test (python=3.8 biopython=1.79)	7m 8s
pathogen-repo-ci (lassa)	45s
test (python=3.8 biopython=1.80)	6m 57s
pathogen-repo-ci (mumps)	52s
test (python=3.8 biopython=latest)	7m 0s
pathogen-repo-ci (ncov)	1m 0s
test (python=3.9 biopython=1.79)	7m 16s
pathogen-repo-ci (seasonal-flu)	1m 1s
test (python=3.9 biopython=1.80)	7m 21s
pathogen-repo-ci (tb)	1m 17s
test (python=3.9 biopython=latest)	7m 36s
pathogen-repo-ci (zika)	47s
test (python=3.10 biopython=1.80)	7m 7s
test (python=3.10 biopython=latest)	7m 9s
test (python=3.11 biopython=1.80)	7m 21s
test (python=3.11 biopython=latest)	7m 12s
build-docs / build-conda	0s
build-docs / build-pip	52s
codecov	13s
	1h 28m 11s

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