jeromekelleher / sc2ts

Infer a succinct tree sequence from SARS-COV-2 variation data
MIT License
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Node 1240908 incorrectly placed in upgma-full-md-30-mm-3-2021-06-30.ts.tsz #80

Open jeromekelleher opened 1 year ago

jeromekelleher commented 1 year ago

This sample is being placed on much too short a branch, which would seem to be a result of a chain of reversions. It would be worth unpicking this to see how these reversions got in (i.e., were they place by parsimony during tree building, and if so, would a better tree building alg have done a better job?)

rogue-b117

hyanwong commented 1 year ago

This is "Kuwait/JAH3090859/2021" as mentioned at https://github.com/jeromekelleher/sc2ts/issues/77#issuecomment-1406963615:

Screenshot 2023-01-27 at 22 47 45