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Hello,
I was trying to use a mouse covid reference, called MA10.
https://www.ncbi.nlm.nih.gov/nuccore/1898953378
I uploaded the fasta file as the new reference. Should I use fasta file as the r…
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While using v3 (master.clades.nextstrain.org) I suddenly got the following error:
```
Error message: Error: The target 'stop-codons-label___index_1849__seqName_hCoV-19-USA-CA-HLX-STM-HVGZFYFHC-2023-…
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Hi! Thanks for the great package, I use parts of it routinely without issue.
I have a question about how to interpret the NAs sometimes outputted in boot.phylo() after using nj(dist(data_matrix)) …
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Hi there,
I just was wondering why I have no output and tried the second example from here:
https://github.com/lenaschimmel/sc2rf#no-output--some-sequences-not-shown
So I added `--clades all --…
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Follow up to #40
With the recent addition of the community H5 Nextclade datasets in https://github.com/nextstrain/nextclade_data/pull/196, it should now be possible to run Nextclade as part of ing…
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As part of https://github.com/tskit-dev/tutorials/issues/182 we should think of alternative ways of showing big trees. One possibility is to collapse clades in a tree if e.g. all the nodes underneath …
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### Context
`augur clades` currently places clades by finding the biggest branches on a tree that satisfy each clades defining mutations as provided by the user.
This method has a few downsides:…
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Right now, the documentation for augur clades is lacking.
The docs section contains nothing but the CLI help: https://docs.nextstrain.org/projects/augur/en/stable/usage/cli/clades.html
There's a…
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Hello,
For input files containing only SNPs, do I need to do anything different? Or Do I just put one site per locus as below:
```
4 1
ind1^pop1 A
ind2^pop1 A
ind3^pop2 T
ind4^po…
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Because ncov clades don't contain aa mutations anymore, I stopped passing aa node data to augur clades.
Turns out this causes an error - somewhat unexpectedly since it'd be possible to check whethe…