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merge: Support single inputs

enhancementNew feature or requestNew feature or request

Status: Open.

#1974 In nextstrain/augur;

· victorlin opened on Mar 23, 2026

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

enhancementNew feature or requestNew feature or request

Status: Open.

#1968 In nextstrain/augur;

· jbloom opened on Mar 2, 2026

multiple inputs: include source attribution

enhancementNew feature or requestNew feature or request

Status: Open.

#1965 In nextstrain/augur;

· jameshadfield opened on Feb 26, 2026

filter: Remove deprecated --output and -o options

breakingMakes a backwards incompatible change and should wait for major releaseMakes a backwards incompatible change and should wait for major release

Status: Open.

#1949 In nextstrain/augur;

· victorlin opened on Jan 23, 2026

Add support to export distances as pairwise distance matrix

enhancementNew feature or requestNew feature or request

Status: Open.

#1931 In nextstrain/augur;

· huddlej opened on Dec 4, 2025

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

bugSomething isn't workingSomething isn't working

enhancementNew feature or requestNew feature or request

treetimeUpstream issue with treetimeUpstream issue with treetime

Status: Open.

#1919 In nextstrain/augur;

· misacodes opened on Oct 25, 2025

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

enhancementNew feature or requestNew feature or request

Status: Open.

#1910 In nextstrain/augur;

· corneliusroemer opened on Oct 11, 2025

Uncaught error in curate transform-strain-name

bugSomething isn't workingSomething isn't working

Status: Open.

#1906 In nextstrain/augur;

· corneliusroemer opened on Oct 10, 2025

Unhandled error in curate apply-geolocation-rules

bugSomething isn't workingSomething isn't working

Status: Open.

#1904 In nextstrain/augur;

· corneliusroemer opened on Oct 10, 2025

Add docs for augur frequencies

documentationImprovements or additions to documentationImprovements or additions to documentation

Status: Open.

#1899 In nextstrain/augur;

· joverlee521 opened on Oct 6, 2025

Add validation of metadata

enhancementNew feature or requestNew feature or request

Status: Open.

#1896 In nextstrain/augur;

· huddlej opened on Oct 3, 2025

align: Improve handling of duplicate reference sequence

enhancementNew feature or requestNew feature or request

Status: Open.

#1892 In nextstrain/augur;

· victorlin opened on Sep 22, 2025