Nextstrain-augur

Bug Fixes

* dependencies: Require the most recent minor versions of TreeTime (0.8.X) to fix numpy matrix errors [633][]

[633]: https://github.com/nextstrain/augur/pull/633

Features

* docs: Migrate non-reference documentation to docs.nextstrain.org [620][]
* filter: Add `--exclude-ambiguous-dates-by` flag to enable exclusion of samples with ambiguous dates [623][] and [631][]

[620]: https://github.com/nextstrain/augur/pull/620
[623]: https://github.com/nextstrain/augur/pull/623
[631]: https://github.com/nextstrain/augur/pull/631

Bug Fixes

* tree: Use a more generic approach to escape special characters from alignment sequence names prior to running IQ-TREE [625][]
* filter: Reduce memory usage by not reading sequences into memory [627][]

[625]: https://github.com/nextstrain/augur/pull/625
[627]: https://github.com/nextstrain/augur/pull/627

Bug Fixes

* refine: Report divergence by number of mutations as an integer instead of a floating point value [618][]
* validate: Allow internal nodes with a single child and do not allow duplicate node names [621][]

[618]: https://github.com/nextstrain/augur/pull/618
[621]: https://github.com/nextstrain/augur/pull/621

Bug Fixes

* align: Remove references to BioPython's deprecated `Alphabet` attributes [615][]
* Pin BioPython dependency to a max supported version to prevent breaking changes to augur in the future [615][]

[615]: https://github.com/nextstrain/augur/pull/615

Bug Fixes

* ancestral: Clarify default values for inference of ambiguous bases [613][]

[613]: https://github.com/nextstrain/augur/pull/613