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blab / nextflu

Real-time tracking of influenza evolution
http://nextflu.org
GNU Affero General Public License v3.0
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proper alignment to root #120

Open rneher opened 8 years ago

rneher commented 8 years ago

replace the current alignment algorithm with something that tolerates gaps

trvrb commented 8 years ago

Can you say more? You'd like an alignment that maintains gaps? Wouldn't numbering get very complicated in this case?

I guess you could do an alignment that allows gaps then build the tree then remove gaps to get canonical numbering.

rneher commented 8 years ago

this refers to the sequence search in javascript. We align to root using a stupid string matching routine and then look for mutations. If the query has a gap relative to root, no proper alignment is found.

trvrb commented 6 years ago

This has been resolved in the nextstrain/augur codebase.

rneher commented 6 years ago

I don't think this is resolved. It also refers to sequence search/alignment in auspice rather than augur. This should be a feature request in auspice. I did write a proper pairwise aligner a while back: https://github.com/neherlab/timetree_viewer/blob/master/js/alignPairwise.js

trvrb commented 6 years ago

I see. Thanks Richard. Just reopened.