Print warnings if alignment names will be changed by IQtree #3305

Job	Run time
check-docs	40s
mypy	58s
pathogen-repo-ci (dengue)	2m 50s
pathogen-repo-ci-v0 (avian-flu)	56s
pathogen-repo-ci (lassa)	8m 5s
pyright	20s
pathogen-repo-ci-v0 (ebola)	55s
pathogen-repo-ci (measles)	1m 36s
pathogen-repo-ci (mpox)	1m 24s
pathogen-repo-ci-v0 (mumps)	54s
test (python=3.9 biopython=1.80)	13m 22s
pathogen-repo-ci (oropouche)	1m 34s
pathogen-repo-ci-v0 (ncov)	1m 0s
test (python=3.9 biopython=1.82)	13m 8s
pathogen-repo-ci (rabies)	4m 35s
pathogen-repo-ci-v0 (rsv)	8m 34s
test (python=3.9 biopython=latest)	13m 11s
pathogen-repo-ci (seasonal-cov)	1m 53s
pathogen-repo-ci-v0 (seasonal-flu)	1m 12s
test (python=3.10 biopython=1.80)	13m 25s
pathogen-repo-ci (wnv)	1m 7s
pathogen-repo-ci-v0 (tb)	1m 16s
pathogen-repo-ci (yellow-fever)	4m 22s
test (python=3.10 biopython=1.82)	13m 23s
pathogen-repo-ci (zika)	1m 12s
test (python=3.10 biopython=latest)	13m 23s
test (python=3.11 biopython=1.80)	13m 24s
test (python=3.11 biopython=1.82)	13m 25s
test (python=3.11 biopython=latest)	13m 24s
test (python=3.12 biopython=1.82)	13m 24s
test (python=3.12 biopython=latest)	13m 23s
build-docs / build	2m 27s
codecov	0s
release	0s
rebuild-docker-image	0s
	3h 14m 42s

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