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CHANGES.md

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## __NEXT__
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### Features
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* clades, export v2: Clade labels + coloring keys are now definable via arguments to augur clades allowing pipelines to use multiple invocations of augur clades resulting in multiple sets of colors and branch labels. How labels are stored in the (intermediate) node-data JSON files has changed. This should be fully backwards compatible for pipelines using augur commands, however custom scripts may need updating. PR [#728][], @jameshadfield.
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[#728]: https://github.com/nextstrain/augur/pull/728
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### Bug Fixes
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* 17.1.0 updated TreeTime to version 0.9.2 and introduced the flag `--use-fft`. This makes previously costly marginal date inference cheaper. This update adjusts when `refine` runs marginal date inference during its iterative optimization. Without the `use-fft` flag, it will now have as it did before 17.1.0 (marginal inference only during final iterations). With the `--use-fft` flag, marginal date inference will be used at every step during the iteration if refine is run with `--date-inference marginal` [#1034][]. (@rneher)

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