Hello Everyone!,
I have a Newick file with cosine distance between different strains of Covid and I’m trying to use auspice for visualization. But I came to know that auspice doesn’t support Newick, so can anybody guide me on how should modify my Newick or create an auspice supported JSON file.
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You should be able to drop the newick onto https://auspice.us, as well as any metadata you have (see help on that page). Let me know if this doesn’t work!
Hello @james, I’m not able to use auspice for my Newick file.
Here is the error message:
I’m sending you my Newick file through direct message to verify. FYI, I’m able to create a dendrogram using this file on ITOL
Hi @Sourabh7211 – the tree you sent me is missing a root-branch length. Defining the root as zero length for your tree allows it to load correctly in auspice.us (i.e. the end of the newick string is 4.17232505e-07):0;).
P.S. This is Newick trees without a root branch length fail to load · Issue #13 · nextstrain/auspice.us · GitHub and will be fixed eventually.
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Thanks, @james. I’m now able to use the Newick file on auspice.
However, if auspice reads JSON files, it should be converting my Newick to JSON, right? If yes, can I get this JSON file with metadata info, because I want to host auspice on my server, I will need a JSON file for that. I tried using augur refine to convert my custom Newick to JSON, but it needs additional parameters like aligned fasta which is not required while I’m dragging and dropping my custom Newick on auspice.us.
Thanks, your help is very much appreciated.
However, if auspice reads JSON files, it should be converting my Newick to JSON, right? If yes, can I get this JSON file with metadata info, because I want to host auspice on my server, I will need a JSON file for that.
Here’s the code auspice.us uses which you could adapt to your use-case.
You should also be able to use augur commands (augur export v2 is what produces the dataset JSON), but as you point out you may need extra files here.
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hello @james
may i jump on this thread?
i’ve successfully imported a newick file and exported the svg - rendered here as a png (2023-02-07_16-38-06.png)
here is the ITOL version: iTOL: Interactive Tree Of Life
how to export the transformation as a json file?
in the online interface, i do not see where to execute an auspice command.
do i need to create an auspice environment to run the augur export v2
thank you for guidance here
/jay
Hi @jay, welcome. There is currently not a way to download the JSON that auspice.us internally produces when you drag on a Newick tree. The augur export v2 command that James referred to does require you install Augur, a part of Nextstrain, yourself. There is not a way to run that command in the context of auspice.us.
You can follow our Nextstrain installation instructions to get access to augur export v2.
Thank you @trs for the quick response.
We’ll install and follow the instructions.
/jay