Issues

• Centralize clades.tsv and masking

  nextstrain/mpox#371 · Filter by author corneliusroemer opened on Jul 21, 2026

• how to select mutaion to make clades.tsv

  documentation
  nextstrain/mpox#366 · Filter by author hanguojun007 opened on Jun 24, 2026
  1

• ingest: Switch PPX URL

  nextstrain/mpox#356 · Filter by author joverlee521 opened on Jan 10, 2026

• ingest/nextstrain-automation: revisit Slack notification rules

  nextstrain/mpox#346 · Filter by author joverlee521 opened on Nov 14, 2025
  2

• ingest: curate PPX geolocation fields

  nextstrain/mpox#345 · Filter by author joverlee521 opened on Nov 13, 2025

• ingest/nextstrain-automation: Uploaded files are double compressed

  nextstrain/mpox#343 · Filter by author joverlee521 opened on Nov 13, 2025
  1

• dead links

  bug
  nextstrain/mpox#332 · Filter by author kapsakcj opened on Aug 15, 2025
  1

• ingest: remove .gz/.xz files and date_submitted column by TBD

  nextstrain/mpox#320 · Filter by author joverlee521 opened on Jun 23, 2025
  3

• Support for nextstrain run

  nextstrain/mpox#314 · Filter by author joverlee521 opened on Jun 11, 2025

• [phylogenetic] B.1 tree fails due to "export: has duplicate nodes or "treetime: nodes with name None"

  bug
  nextstrain/mpox#310 · Filter by author corneliusroemer opened on Apr 23, 2025
  4

• Relax Nextclade dataset coverage thresholds

  nextstrain/mpox#308 · Filter by author corneliusroemer opened on Mar 19, 2025

• assign-colors scripts are largely identical

  nextstrain/mpox#286 · Filter by author jameshadfield opened on Nov 3, 2024
  2

• Reached maximum recursion depth when building phylogenetic trees

  bug
  nextstrain/mpox#282 · Filter by author mengfeip opened on Oct 20, 2024
  3

• Update phylogenetic GH Action workflows

  nextstrain/mpox#259 · Filter by author joverlee521 opened on Jun 18, 2024

• Potentially include year-only sequences

  enhancement
  nextstrain/mpox#231 · Filter by author corneliusroemer opened on Jan 21, 2024

• Reverse complement reverse-complemented sequences in ingest to reduce downstream complications

  enhancement
  nextstrain/mpox#192 · Filter by author corneliusroemer opened on Sep 22, 2023
  1

• Support for GISAID data

  documentation
  nextstrain/mpox#63 · Filter by author huddlej opened on Jun 16, 2022
  4

• ingest: deduplicate sequences using strain names

  enhancement
  nextstrain/mpox#33 · Filter by author joverlee521 opened on Jun 7, 2022
  1

• ingest: canonicalize strain names

  enhancement
  nextstrain/mpox#32 · Filter by author joverlee521 opened on Jun 7, 2022
  1