Issues

• Read color odering directly in augur export v2

  enhancement
  nextstrain/augur#2045 · Filter by author jameshadfield opened on Aug 31, 2026
  1

• distance: Add option to calculate the cumulative distance from the root node to each tip instead of the pairwise distance

  enhancement
  nextstrain/augur#2035 · Filter by author huddlej opened on Aug 3, 2026
  1

  

• docs: Fix numpy types for Python 3.12

  documentation
  nextstrain/augur#2017 · Filter by author joverlee521 opened on Jun 22, 2026
  4

• io/metadata: increase csv.field_size_limit

  nextstrain/augur#2013 · Filter by author joverlee521 opened on Jun 17, 2026
  2

• [export] Allow warning text in auspice-config JSON

  enhancement
  nextstrain/augur#2012 · Filter by author jameshadfield opened on Jun 15, 2026

• refine: simplify node data JSON output

  nextstrain/augur#2010 · Filter by author joverlee521 opened on Jun 4, 2026
  1

  

• Config based Augur commands

  enhancement
  nextstrain/augur#1987 · Filter by author joverlee521 opened on May 4, 2026
  5

  

• [refine] ? allow substitution model selection

  enhancement
  nextstrain/augur#1982 · Filter by author jameshadfield opened on Apr 7, 2026

• is there a way to give protein sites non-sequential numbering?

  enhancement
  nextstrain/augur#1968 · Filter by author jbloom opened on Mar 2, 2026
  3

• multiple inputs: include source attribution

  enhancement
  nextstrain/augur#1965 · Filter by author jameshadfield opened on Feb 26, 2026
  5

• filter: Remove deprecated --output and -o options

  breaking
  nextstrain/augur#1949 · Filter by author victorlin opened on Jan 23, 2026

• Unhelpful error message from treetime when augur ancestral fails to load translation alignment

  bugenhancementtreetime
  nextstrain/augur#1919 · Filter by author misacodes opened on Oct 25, 2025
  1

• Optionally error if not all clades defined in clades.tsv are found in tree

  enhancement
  nextstrain/augur#1910 · Filter by author corneliusroemer opened on Oct 11, 2025
  1

• Uncaught error in curate transform-strain-name

  bug
  nextstrain/augur#1906 · Filter by author corneliusroemer opened on Oct 10, 2025
  1

• Unhandled error in curate apply-geolocation-rules

  bug
  nextstrain/augur#1904 · Filter by author corneliusroemer opened on Oct 10, 2025
  3

• Add docs for augur frequencies

  documentation
  nextstrain/augur#1899 · Filter by author joverlee521 opened on Oct 6, 2025

• Add validation of metadata

  enhancement
  nextstrain/augur#1896 · Filter by author huddlej opened on Oct 3, 2025

• align: Improve handling of duplicate reference sequence

  enhancement
  nextstrain/augur#1892 · Filter by author victorlin opened on Sep 22, 2025
  3

• subsample: Improve --output-log

  enhancement
  nextstrain/augur#1886 · Filter by author victorlin opened on Sep 16, 2025
  1

• merge: Support inner join

  enhancement
  nextstrain/augur#1873 · Filter by author victorlin opened on Jul 28, 2025

• merge: Unhelpful error message with named sequence inputs

  bug
  nextstrain/augur#1867 · Filter by author victorlin opened on Jul 23, 2025

• augur align: inserted Ns are reported incorrectly

  bug
  nextstrain/augur#1864 · Filter by author tomalf2 opened on Jul 23, 2025
  3

• When we switch to Python 3.14, collect coverage with COVERAGE_CORE=sysmon

  nextstrain/augur#1862 · Filter by author corneliusroemer opened on Jul 20, 2025
  1

• Deprecation warning in curate: "Parsing dates involving a day of month without a year specified is ambiguious"

  bug
  nextstrain/augur#1858 · Filter by author corneliusroemer opened on Jul 19, 2025
  1

• Deprecation warning in export.py: "Nesting mutually exclusive groups is deprecated."

  bug
  nextstrain/augur#1854 · Filter by author corneliusroemer opened on Jul 15, 2025