Using influenza datasets in clades.nextstrain.org

Hello, I have experience using https://clades.nextstrain.org/ for SARS-CoV-2 genome sequence analysis, but am having difficulty with influenza A.

I am trying to use it primarily to identify mutations in partial HA and NA fragments.

Whereas for SARS-CoV-2, you can upload a partial sequence (e.g. partial spike gene fragment) and get a result, when I try to do it with different influenza A reference sets, it gives error messages saying “Unable to align: seed alignment was unable to find any matches that are long enough.”

I tried using a full-length NA segment against the Influenza A H1N1pdm NA reference dataset, and it still gave the same error.

Is it necessary to have the full-length HA or NA sequence for it to work?

Thank you in advance,
Jose

hi @jmediavi

partial sequences for HA and NA should definitely work. Could you share one such example?

richard