I am new here. I would like to get the ancestral sequences for viruses in the online virus data in nexstrain.org.
I was not able to find these so I was thinking I run only the treetime step? I download GenBank files and aligned them but now I can not figure out how I can get the --dates file needed to run treetime.
I would appreciate your help. Thank you!
Hi! The most straightforward way would be to run
augur ancestral - which is how we do the ancestral reconstruction in practice (it calls treetime under the hood): augur ancestral — Augur 21.0.0 documentation
You can also piece ancestral sequences together by looking at the tree.json file.
A pretty simple pipeline that shows how things are done in practice is here: monkeypox/core.smk at b54768ec17872eb0d898e29527785642f6b98c0d · nextstrain/monkeypox · GitHub
Thanks. I can not figure out how to crate tree.json with augur ancestral I only found output-node-data.json.
How can I get a tree file with internal nodes?