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Update changelog
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victorlin committed Jan 12, 2024
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* separate VCF-only arguments into their own group
* translate: Fixes a bug in the parsing behaviour of GFF files whereby the presence of the `--genes` command line argument would change how we read individual GFF lines. Issue [#1349][], PR [#1351][] (@jameshadfield)
* If `TreeTimeError` is encountered Augur now exits with code 2 rather than 0. (This restores the original behaviour.) [#1367][] (@jameshadfield)
* ancestral, translate: Avoid incompatibilities with Biopython 1.82. [#1374][] (@victorlin)
* ancestral, translate: Avoid incompatibilities with Biopython >=1.82. [#1374][], [#1387][] (@victorlin)
* ancestral, translate: Address Biopython deprecation warnings. [#1379][] (@victorlin)
* ancestral: Previously, the help text for `--genes` falsely claimed that it could accept a file. Now, it can truly claim that. [#1353][] (@victorlin)
* Deprecate `read_strains` from `augur.utils` and add it to the public API under `augur.io`. [#1353][] (@victorlin)
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[#1379]: https://github.com/nextstrain/augur/pull/1379
[#1352]: https://github.com/nextstrain/augur/pull/1352
[#1353]: https://github.com/nextstrain/augur/pull/1353
[#1387]: https://github.com/nextstrain/augur/pull/1387

## 23.1.1 (7 November 2023)

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