# Where can I look up clade defining mutations for seasonal flu?

**URL:** <https://nextstrain.discourse.group/t/where-can-i-look-up-clade-defining-mutations-for-seasonal-flu/1229>\
**Category:** Help and Getting Started\
**Created:** [August 31, 2022, 3:30pm UTC](https://nextstrain.discourse.group/t/where-can-i-look-up-clade-defining-mutations-for-seasonal-flu/1229 "2022-08-31T15:30:51Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![corneliusroemer](https://yyz1.discourse-cdn.com/flex031/user_avatar/nextstrain.discourse.group/corneliusroemer/32/175_2.png) [@corneliusroemer](https://nextstrain.discourse.group/u/corneliusroemer)\
**Post date:** [August 31, 2022, 3:30pm UTC](https://nextstrain.discourse.group/t/where-can-i-look-up-clade-defining-mutations-for-seasonal-flu/1229/1 "2022-08-31T15:30:51Z")

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_This is a Q&A that happened privately that I’m open sourcing for future reuse_

> I am using NextStrain to assign clades to the H1N1 viruses in my dataset, but I noticed there were many unassigned viruses. For the H1N1 clades prior to 2014 that aren’t assigned by Nextclade, could you share the criteria NextStrain uses to define these pre-2014 clades (e.g., clade 7) so I could apply the same criteria to my data and be consistent with NextStrain?

The clade defining mutations are contained in the `clades.tsv` file in the seasonal-flu repo [https://github.com/nextstrain/seasonal-flu/blob/master/config/clades\_h1n1pdm\_ha.tsv](https://github.com/nextstrain/seasonal-flu/blob/master/config/clades_h1n1pdm_ha.tsv)

If you are making a build using augur tools, you can assign these clades using the `augur clades` command using that `clades.tsv` from above: [augur clades — Augur 23.1.1 documentation](https://docs.nextstrain.org/projects/augur/en/stable/usage/cli/clades.html)

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**Author:** ![Thomas](https://avatars.discourse-cdn.com/v4/letter/t/e36b37/32.png) [@Thomas](https://nextstrain.discourse.group/u/Thomas)\
**Post date:** [February 4, 2025, 2:35pm UTC](https://nextstrain.discourse.group/t/where-can-i-look-up-clade-defining-mutations-for-seasonal-flu/1229/2 "2025-02-04T14:35:32Z")

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Hi Cornelius,

Thank you for posting this. Does this list only contain the mutations that were used to define the clades? For RSV, you had a more extensive list of amino acids reaching \>=90% in clades, published in the unified proposal for classification of human RSV below the subgroup level. Is a more complete list also available for flu? Now that I look at it more closely, it seems the clades genome file for RSV is organized hierarchically ([rsv/config/clades\_genome\_a.tsv at master · nextstrain/rsv · GitHub](https://github.com/nextstrain/rsv/blob/master/config/clades_genome_a.tsv)), vs the HA file for flu is not ([seasonal-flu/config/h1n1pdm/ha/clades-long.tsv at master · nextstrain/seasonal-flu · GitHub](https://github.com/nextstrain/seasonal-flu/blob/master/config/h1n1pdm/ha/clades-long.tsv)).

Thank you!  
Thomas