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)