-
-
@stamatak I want to compare the placement with the reference tree. But I have no idea about how to convert the format to the newick? Looking forward to your reply!
-
Hi!
I got this error when running:
epa-ng
-t reference_tree.raxml.bestTree
-s reference_aligment.fasta
-q query.fasta
-w ./ --model reference_tree.raxml.bestModel
Please find …
-
This sequence has mostly Ns with 1 mutation and is "recombinant". Just checking that this is intended behavior. Certainly a little confusing.
-
There are a large number of sequences in GISAID that GISAID tags with Omicron lineage and a Pango lineage such as BA.1 / BA.1.1 but which have collection and submission dates predating the Omicron dis…
-
Hello, I'm tryting to run epa-ng with a newick tree generated with ETE3 (previously resolving the polytomies) and I recieve this error:
terminate called after throwing an instance of 'std::runtime…
-
Copied over from https://github.com/cov-lineages/pangolin/issues/253
Dear Pangolin team,
When assigning lineages to patient samples with pangolin I stumbled over a cluster that looks like B.1.62…
-
Hey Lucas,
I ran into something that I do not fully understand regarding the prediction of the LCA with gappa edit accumulate.
I have placements on a phylogenetic tree through EPA-ng for the seque…
-
I was wondering if we could have access to the placement file that SEPP produces when running deblur. The placement file has information regarding placement uncertainty (for example, look at here http…
-
### Summary
- What does this package do? (explain in 50 words or less):
This package helps users to build a reasonable starting phylogeny for phylogenetic analysis.
In particular, this package…