5.0.0

5.0.0 (26 May 2019)

Features

• ancestral: New option to --keep-ambiguous, which will not infer nucleotides at
  ambiguous (N) sites on tip sequences and instead leave as 'N'
  See PR 280.
• ancestral: New option to --keep-overhangs, which will not infer nucleotides for
  gaps on either side of the alignment and instead leave as '-'.
  See PR 286.
• clades: This module has been reconfigured to identify clade defining mutations on
  top of a reference rather than identifying mutations along the tree. The command
  line arguments are the same except for the addition of --reference, which
  explicitly passes in a reference sequence. If --reference is not defined, then
  reference will be drawn from the root node of the phylogeny by looking for
  sequence attribute attached to root node of --tree.
  See PR 288.
• refine: Revise rooting behavior. Previously --root took 'best', 'residual', 'rsq'
  and 'min_dev' as options. In this update --root takes 'best', least-squares',
  'min_dev' and 'oldest' as rooting options. This eliminates 'residual' and 'rsq'
  as options. This is a backwards-incompatible change. This requires updating
  TreeTime to version 0.5.4 or above.
  See PR 263.
• refine: Add --keep-root option that overrides --root specification to preserve
  tree rooting.
  See PR 263.
• refine: Add --covariance and --no-covariance options that specify TreeTime
  behavior.
  See PR 263.
• titers: This command now throws an InsufficientDataException if there are not
  sufficient titers to infer a model. This is paired with a new --allow-empty-model
  flag that proceeds past the InsufficientDataException and writes out a model
  JSON corresponding to an 'empty' model.
  See PR 281.
• By default JSONs are written with index=1 to give a pretty-printed JSON. However,
  this adds significant file size to large tree JSONs. If the environment variable
  AUGUR_MINIFY_JSON is set then minified JSONs are printed instead. This mirror the
  explicit --minify-json argument available to augur export.
  See PR 278.

Bug fixes

• export: Cast numeric values to strings for export.
  See issue 287.
• export: Legend order preserves ordering passed in by user for traits that have
  default colorings ('country' and 'region').
  See PR 284.
• refine: Previously, the --root argument was silently ignored when no timetree
  was inferred. Re-rooting with an outgroup is sensible even without a timetree.
  See PR 282.