Assigned Clade different from Clade of assigned node

[taeschbacher-gilead]

I queried a RSVA sequence using the nextclade using the web interface.

It seems that the sequence was added to a node with clade A.D.3.3. The clade that was assigned to the sequence is A.D.3. Is this an issue or am I not interpreting this correctly? The sequence is the one at the bottom of the attached figure with name PP352363_L.

This is the fasta file:
seq.txt

[rneher]

Thanks for raising this, @taeschbacher-gilead !

Nextclade first finds the closest match on the fixed reference tree for each sequence and assigns the clade based on this match. Only after all sequences are assigned to clades, the tree is modified by introducing additional internal nodes to improve the placement of the query sequences.

The inconsistency you observe is due to the simplistic way nextclade currently labels newly created internal nodes. It currently uses the clade annotation of the child node of the branch that is being split (A.D.3.3 in this case), even though the sibling (your query sequence) is assigned A.D.3. We are working on ways to make the clade assignment of new internal nodes more consistent.

thanks again for pointing this out!
richard

[taeschbacher-gilead]

Thank you, Richard, for the fast reply!

[ivan-aksamentov]

This has been addressed in #1526 and released in 3.9.1