Implement pango lineage placements using consensus genomes#26
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trongnhanuit wants to merge 28 commits into
Open
Implement pango lineage placements using consensus genomes#26trongnhanuit wants to merge 28 commits into
trongnhanuit wants to merge 28 commits into
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trongnhanuit
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Mar 19, 2025
trongnhanuit
commented
- Implement lineage assignments by finding placements for lineage consensus genomes.
- Compute SPRTA supports for plausible placements of each lineage.
- Parallelize lineage assignments with joblib
…'t add the new sample as a minor sequence
… were misclassified as redundant placement
…a subtree if l1 (the appending branch length) <= 1 mutation
…age placement on the top of the polytomy
…acements of multiple lineages, we allow assigning all of these lineages (or only the closet lineage) to the subtree
…undant except a few special cases
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