* frequencies: Include `counts` in `augur frequencies` output JSON to support downstream plotting.
Data
* Include additional country lat/longs in base data
3.1.3
Features
* filter: Add `--non-nucleotide` option to remove sequences with non-conforming nucleotide characters.
Bug fixes
* Revise treatment of `-`, ` ` in `augur parse` to leave `-` as is and remove white space. Also delimit `[` and `]` to `_`. * Fix bug in naming of temp IQTREE fixes to prevent conflicts from simultaneous builds.
Data
* Include additional country lat/longs in base data
Development
* Remove non-modular measles build in favor of [nextstrain/measles](https://github.com/nextstrain/measles) repo.
3.1.2
Bug fixes
* Update dependencies
3.1.1
Bug fixes
* filter: Fix `--include-where`. Adds an `all_seq` variable needed by the logic to include records by value. This was previously working for VCF but threw an exception for sequences in FASTA format. * Update flu reference viruses and lat longs. * Update dependencies
3.1.0
Features
* reconstruct-sequences: Include `augur reconstruct-sequences` module that reconstructs alignments from mutations inferred on the tree * distance: Include `augur distance` module that calculates the distance between amino acid sequences across entire genes or at a predefined subset of sites * lbi: Include `augur lbi` module that calculates local branching index (LBI) for a given tree and one or more sets of parameters. * frequencies: Include `--method kde` as option to `augur frequencies`, separate from the existing `--method diffusion` logic. KDE frequencies are faster and better for smaller clades but don't extrapolate as well as diffusion frequencies. * titers: Enable annotation of nodes in a tree from the substitution model
3.0.5.dev1
Bug fixes
* translate: Nucleotide ("nuc") annotation for non-bacterial builds starts at 0 again, not 1, fixing a regression.
Documentation
* Schemas: Correct coordinate system description for genome start/end annotations.