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Following @wasade 's suggestions in PR #50 as well as other thoughts, I tested multiple options of the `find_lca` function. Benchmarks were performed on a Bowtie2 alignment file of 100,000 lines again…
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There seems to be a large KP.3.1.1+S:S31F branch, while KP.3.1.1 shall have S:31del.
That branch is driven by Denmark seqs which do not handle S:S31del well. When Querying C12616T, A13121T, C2165…
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### Are you using the latest version of the plugin?
- [X] I have verified that I am using the latest version
### Have you checked for similar issues?
- [X] I have verified that there are no similar…
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Defining mutations:
KP.2 > Orf1a:P1803L (C5673T = PLPro_P240L) > C14220T > S:I934V (A24362G) > T931A, G8872A, S:N30K (T21652G)
Query: T931A,C5673T,G8872A
Samples: 7 ( 6 on Gisaid)
Countries: C…
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### Current Behavior
When I run refine with data that's somehow not according to requirements (will figure out how), refine throws an uncaught error
```
TypeError: '
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KR.1 got its DeFLiRT sublineage likely in Philippines
Defining mutations: KR.1 >> C6568T > C6388T, S:S31del (del21653-55)
(New) Query: C6568T,C6388T,T3565C,C897A (by @aviczhl2 )
Samples: 3
Countr…
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# Description
So far, there are patches for Android versions 10 through 13. I would like to build A14 based roms with signature spoofing support; however I am at a loss at how the patches located h…
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Hi developers,
This is a great tool to study convergent evolution. I have several questions:
1. RERcoverge requires that all gene trees have the same topology (same with the species tree if I un…
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From branch 115 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1253
JN.1+C23039G, T22928C, C21627A(S:T22N, F456L, Q493E)
Or JN.1.16+C23039G,C21627A(S:T22N,Q493E)
Now usher…
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`2^16=65536` would be a good cutoff. This is computationally feasible and supports all currently used systems by a wide margin