How to use Nextstrain seasonal flu graph as reference tree for Nextclade?

To Whom It May Concern,

Hi, my name is Isaac, and I am currently pursuing my undergraduate studies in bioinformatics in Malaysia. I am writing to you today because I have been assigned the exciting task of utilizing Nextstrain’s seasonal flu phylogenetic tree ( auspice ) as a reference to analyze and predict vaccine coverage using my own sequences. I am curious to know if it is feasible for me to incorporate my personal sequences into the existing tree and align them using Nextclade. Your guidance and support in this matter would be greatly appreciated. Thank you for taking the time to consider my inquiry, and I look forward to your response.


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Hi Isaac,

Thanks for reaching out and apologies for the delay in responding.

I don’t think the seasonal-flu workflow supports adding your own data to an existing tree in a very simple way. You can always fork the repo and make changes to the workflow - this requires understanding snakemake.

Adding your own existing sequences to an existing tree is a feature that will become available as part of Nextclade version 3 - which we are going to release in around a month. The Nextclade tree builder uses stepwise addition of sequences based on parsimony and does not do any subtree-prune-regraft steps. You can give it a try here:

Let me know if you have further questions.