3.1.7

3.1.7 (5 February 2019)

Bug fixes

• Update to TreeTime 0.5.3
• tree: Fix bug in printing causing errors in Python versions <3.6
• tree: Alter site masking to not be so memory intensive

3.1.6

3.1.6 (29 January 2019)

Features

• filter: Allow negative matches to --exclude-where. For example,
  --exclude-where country!=usa would exclude all samples where metadata country does
  not equal usa.
• tree: Allow --exclude-sites to work with FASTA input. Ensure that indexing of input
  sites is one-based.

Bug fixes

• fix loading of strains when loading titers from file, previously strains had not been
  filtered to match the tree appropriately

3.1.5

3.1.5 (13 January 2019)

Features

• frequencies: Add --ignore-char and --minimal-clade-size as options.
• frequencies: Include --stiffness and --inertia as options.
• titers: Allow multiple titer date files in --titers import.

Bug fixes

• filter: Fix --non-nucleotide call to include ? as allowed character.
• tree: Fix --method raxml to properly delimit interim RAxML output so that
  simultaneous builds don't conflict.

Data

• Include additional country lat/longs in base data

3.1.4

3.1.4 (1 January 2019)

Bug fixes

• frequencies: Include counts in augur frequencies output JSON to support
  downstream plotting.

Data

• Include additional country lat/longs in base data

3.1.3

3.1.3 (29 December 2018)

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 repo.

3.1.2

3.1.2 (21 December 2018)

Bug fixes

• Update dependencies

3.1.1

3.1.1 (21 December 2018)

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

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.