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nextstrain / auspice

Web app for visualizing pathogen evolution
https://docs.nextstrain.org/projects/auspice/
GNU Affero General Public License v3.0
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Sequence search #27

Open rneher opened 7 years ago

rneher commented 7 years ago

search the node in the tree with the closest sequence. In general, this requires pairwise alignment. I implemented a banded pairwise alignment here: https://github.com/neherlab/timetree_viewer/blob/master/js/alignPairwise.js

not tested extensively but in contrast to our current version, this should be able to handle gaps.

trvrb commented 7 years ago

I think this would eventually be useful, however, I'm leaving it in backlog for the moment.

rneher commented 4 years ago

@jameshadfield this says "revisit sometime". I was just thinking again this would be useful to have, I.e. paste a new CoV sequence into the tree, highlight the closest virus, and show the differences. But for this to work, we would need to load the root-sequence.json. What would it take to make this available? It would then happily work in the banded alignment.

jameshadfield commented 4 years ago

Not much & this is needed for us to colour by genotype for positions with no mutations. I'll sketch out an implementation this week.