-
Running these tools in default UShER mode.
- pangolin v4.0.6
- pangolin-data v1.8
- constellations v0.1.9
- scorpio v0.3.17
Many sequences that should be XD (labelled clade GKA on GISAID) are g…
-
## Branch 1: JN.1.4.5+S:S31F, R346T, F456L on C28948T branch
JN.1.4.5> C28948T> C21654T(S:S31F), G22599C(S:R346T), T22928C(S:F456L)
It's placed on a JN.1.4> C5284T> T22928C> G22599C> T5284Crev branc…
-
When we have 3 (or more) way recombinants we sometimes jump to different parents when it's equally likely that we could jump back to the original sequence. The HMM is just choosing arbitrarily from th…
-
KP.2.3 has a mutation on Orf3a:67 which is close to this Orf3a:66. It also appears simutaneously in multiple GBW samples from different countries, so make an issue.
KP.3.2.4+A10558T+C29218T+A25590…
-
One of the largest artefactual recombinants in the alpha version of the sc2ts trees (node 601947 in upgma-full-md-30-mm-3-2021-06-30-il.ts.tsz) is the direct result (seemingly) of reversion pushing n…
-
Hi, I've noticed that sc2rf.py (version sc2rf-7427d2f94b69c965362034c2597b643c5dfaa1cf) could not find any recombination for XT samples available on GISAID `python sc2rf.py nextclade.aligned_XT_Gisaid…
-
Having hyphens in the organization name breaks the flask mapping for the template view function:
```
@recombinant.route('/recombinant-template/__.xlsx', methods=['GET', 'POST'])
```
I suppose hy…
-
Just two sequences but featuring four spike mutations worth proposing it here.
Defining mutations:
XDV.1.8 >> T9892G > A23971G, A9715T, Orf1a:A3615V (C11109T), S:A67G (C21762G), S:N148T (A22005C)…
-
### Motivation
@Taepper, @chaoran-chen and I have discussed generalizing the Pango wildcard search feature, as monophyletic clade search is important (non-wildcard searches are [paraphyletic](https…
-
We can compute the breakpoint interval for a recombinant much more quickly than rerunning the HMM by just comparing the sequences of the two parents. We are by definition just taking the interval wher…