Issues

• Wrong M2-2 annotation used causing lineages with M2-2 defining mutations not to appear, e.g. A.D.3.11

  bug
  nextstrain/rsv#131 · Filter by author corneliusroemer opened on Jun 5, 2026

• Add keep_all option for additional_inputs and sequence_source column

  enhancement
  nextstrain/rsv#122 · Filter by author jbloom opened on Mar 9, 2026
  2

  

• phylo: drop rule rename_and_ready_for_nextclade

  nextstrain/rsv#96 · Filter by author jameshadfield opened on Aug 11, 2025
  1

• phylo: Replace set_final_strain_name.py

  enhancement
  nextstrain/rsv#95 · Filter by author joverlee521 opened on Aug 11, 2025
  2

• Update repo structure to match pathogen-repo-guide

  source: office hours
  nextstrain/rsv#77 · Filter by author joverlee521 opened on Mar 13, 2025

• Properly handle CSV-like TSVs

  nextstrain/rsv#74 · Filter by author joverlee521 opened on Dec 6, 2024

• Rename master to main

  enhancement
  nextstrain/rsv#63 · Filter by author genehack opened on Jun 11, 2024

• Add --start and --end flags to newreferences.py to allow for creating subgenic tree builds

  enhancement
  nextstrain/rsv#56 · Filter by author j23414 opened on Mar 12, 2024

• Add detailed usage docs

  documentationsource: office hours
  nextstrain/rsv#44 · Filter by author joverlee521 opened on Oct 26, 2023