proper alignment to root

[rneher]

replace the current alignment algorithm with something that tolerates gaps

[trvrb]

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]

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]

This has been resolved in the nextstrain/augur codebase.

[rneher]

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]

I see. Thanks Richard. Just reopened.