3.1.0

3.1.0 (18 December 2018)

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

3.0.5.dev1 (26 November 2018)

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.