Cornelius Roemer

ENH: Display all maximally parsimonious locations in web interface, not just 1

4

When I tried to place two sequences they showed 4/8 maximally parsimonious placements. However, there seems to be only 1 subtree for each with 1 placement. How is this placement...

[Enhancement] Don't delete trees or allow manual 'save' so that links don't break after few weeks

1

Usher trees are very useful and are used a lot in pango designation issues. Unfortunately, the builds are removed after a few weeks, causing links to break. Would it be...

[Enhancement] List assigned pango lineage for uploaded samples as coloring on Auspice tree

2

It would be great if you could find Usher (and pangolin default) assigned pango lineages for uploaded samples on the Auspice tree viz. You currently have that information but you...

Stop codons are chopped off in Auspice.json export, ORF8:Q27* wrongly displayed as ORF8:Q27

7

I spotted this weird mutation ORF8:Q27 which missed the target of the mutation.  https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_8534_6af60.json?label=nuc%20mutations:G24410A It turns out, that it should be a stop codon here ORF8:Q27* so it looks...

Inconsistent usage of ORF1ab vs ORF1a/b in Usher's Auspice visualization

8

I love Usher, it's so useful. I'm not sure whether this is the right repo to open this issue, so please refer me on if this is not the right...

Many sequences missing, like USA/PA-VSP3406/2021

1

When uploading sequences to Usher, I often get an error message/warning saying that at least some sequences weren't found. What's the reason for this? Am I doing anything wrong? I...

### Command description Used extensively to assign lineages to SARS-CoV-2 sequences ### Command details 4 ### OS - [ ] Android - [X] Linux - [X] macOS - [ ]...

page request: mamba

2

### Command description Mamba is a fast drop-in replacement for the conda environment manager ### Command details _No response_ ### OS - [ ] Android - [X] Linux - [X]...

### Command description https://github.com/simonw/csv-diff ### Command details _No response_ ### OS - [ ] Android - [X] Linux - [X] macOS - [ ] sunOS - [X] Windows

### Command description Important for python packaging https://github.com/pypa/twine ### Command details _No response_ ### OS - [ ] Android - [X] Linux - [X] macOS - [ ] sunOS -...