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Commits on Sep 25, 2018
  1. Updates to flu reference viruses

    trvrb committed Sep 25, 2018
Commits on Sep 24, 2018
  1. Update H3N2 outliers

    trvrb committed Sep 24, 2018
Commits on Sep 23, 2018
  1. Don't annotate fitness

    trvrb committed Sep 23, 2018
Commits on Sep 21, 2018
  1. Update readme to clarify that IQTREE is default tree builder

    trvrb committed Sep 21, 2018
Commits on Sep 17, 2018
  1. Subset titer matrix to sera with homologous titer >80

    trvrb committed Sep 17, 2018
Commits on Sep 16, 2018
  1. Update flu build

    trvrb committed Sep 16, 2018
    * Add H3N2 outlier
    * Update H1N1pdm and Vic clades
Commits on Sep 15, 2018
  1. Update H3N2 outliers

    trvrb committed Sep 15, 2018
  2. Update Vic clades

    trvrb committed Sep 15, 2018
  3. Update H1 clades

    trvrb committed Sep 15, 2018
Commits on Sep 13, 2018
  1. Move Japan/Korea into Asia deme

    trvrb committed Sep 13, 2018
Commits on Sep 12, 2018
  1. Redo Vic clades

    trvrb committed Sep 12, 2018
  2. Update flu build

    trvrb committed Sep 12, 2018
    * Move japan_korea to separate frequencies bin
    * Add more H1 reference viruses
  3. Include clade_membership as filter for flu builds

    trvrb committed Sep 12, 2018
  4. Include South America in regions list

    trvrb committed Sep 12, 2018
    This absence was causing "SA" to be absent from frequencies.json.
Commits on Sep 11, 2018
  1. Revise Vic deletion variant clade

    trvrb committed Sep 11, 2018
Commits on Sep 9, 2018
  1. Update H1N1pdm reference viruses

    trvrb committed Sep 9, 2018
    Need phylogenetic context to resolve clades 183P.1 and 183P.2
  2. Revise Vic clades

    trvrb committed Sep 9, 2018
  3. Include additional H1N1pdm clades

    trvrb committed Sep 9, 2018
  4. Adjustments for titer matrix plots for H3N2

    trvrb committed Sep 9, 2018
    Update virus clades and serum clades
Commits on Sep 2, 2018
  1. Include more default lat/longs

    trvrb committed Sep 2, 2018
Commits on Sep 1, 2018
  1. Merge pull request #209 from nextstrain/remove-old-builds

    trvrb committed Sep 1, 2018
    Remove ebola, lassa, tb, WNV, and zika builds now in their own repos
  2. Merge pull request #211 from nextstrain/export-safety-checks

    trvrb committed Sep 1, 2018
    Export: Add safety checks for annotations and geo
  3. Export: Add safety checks for annotations and geo

    trvrb committed Sep 1, 2018
    When exporting BEAST trees (or generally trees that haven't passed through augur geo traits and augur translate), we lack "annotations" or "geo". This adds safety checks to only attempt to include "annotations" and "geo" when actually present.
Commits on Aug 22, 2018
  1. Improve Python 2/3 compatibility

    trvrb committed Aug 22, 2018
    These are fixes that arose when running flu.process.py
  2. Include additional clades in titer matrix plots

    trvrb committed Aug 22, 2018
Commits on Aug 20, 2018
  1. Fix clade 3b annotation

    trvrb committed Aug 20, 2018
    Reversion at site 158 was causing live H3N2/2y build to incorrectly annotate clade 6b onto recent viruses.
Commits on Aug 16, 2018
  1. Improve 2/3 compatibility in io_util.py

    trvrb committed Aug 16, 2018
    This was necessary to run json_to_tree in Python 3.
Commits on Aug 12, 2018
  1. Update flu clade designations

    trvrb committed Aug 12, 2018
    This is mostly a linting pass to improve whitespace and alignment. It does however correct an issue with repeated 3c2 clade designations and fix the Vic DV designation.
Commits on Aug 11, 2018
  1. Update flu reference viruses

    trvrb committed Aug 11, 2018
    This needs periodic updating to keep reference viruses in 2y builds.
Commits on Aug 9, 2018
  1. Merge pull request #198 from nextstrain/fix-ep-mutations

    trvrb committed Aug 9, 2018
    Exclude undetermined residues from amino acid mutation counts
  2. Merge pull request #174 from nextstrain/na-epitope-mask

    trvrb committed Aug 9, 2018
    Added support for NA epitope and non-epitope mutations
Commits on Aug 5, 2018
  1. Small fix to date filter for ambiguous dates

    trvrb committed Aug 5, 2018
    Cherry picked from @rneher's commit 2d68b83
  2. Include Taiwan in lat/longs

    trvrb committed Aug 5, 2018
  3. Make file name the same as augur call

    trvrb committed Aug 5, 2018
    Avoiding the extra redirection
Commits on Aug 1, 2018
  1. Further updates to flu outliers

    trvrb committed Aug 1, 2018
    Bunch of new H3N2v viruses from 2012 appeared in GISAID