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version 6.3.0

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trvrb committed Feb 13, 2020
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## __NEXT__


## 6.3.0 (13 February 2020)

### Features

* Augur `refine`, `ancestral` and `traits` now use the
[upgraded TreeTime v0.7](https://github.com/neherlab/treetime/releases/tag/v0.7.0)
This should have a number of under-the-hood improvements.
[See PR 431](https://github.com/nextstrain/augur/pull/431)
* ancestral: New options to either `--keep-ambiguous` or `--infer-ambiguous`. If using
`--infer-ambiguous` the previous behavior will be maintained in which tips with `N` will have
their nucleotide state inferred. If using `--keep-ambiguous`, these tips will be left as `N`.
With this upgrade, we are still defaulting to `--infer-ambiguous`, however, we plan to swap
default to `--keep-ambiguous` in the future. If this distintion matters to you, we would suggest
that you explicitly record `--keep-ambiguous` / `--infer-ambiguous` in your build process.
[Also part of PR 431](https://github.com/nextstrain/augur/pull/431)
* traits: Allow input of `--weights` which references a `.tsv` file in the following format:
```
division Hubei 10.0
division Jiangxi 1.0
division Chongqing 1.0
```
where these weights represent equilibrium frequencies in the CTMC transition model. We imagine the
primary use of user-specified weights to correct for strong sampling biases in available data.
[See PR 443](https://github.com/nextstrain/augur/pull/443)

### Bug fixes

* Improvements to make shell scripts run more easily on Windows.
[See PR 437](https://github.com/nextstrain/augur/pull/437)

## 6.2.0 (25 January 2020)

### Features
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__version__ = '6.2.0'
__version__ = '6.3.0'

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