# Ancestral sequences

**URL:** <https://nextstrain.discourse.group/t/ancestral-sequences/1332>\
**Category:** Help and Getting Started\
**Created:** [February 12, 2023, 12:40pm UTC](https://nextstrain.discourse.group/t/ancestral-sequences/1332 "2023-02-12T12:40:15Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![EHC](https://avatars.discourse-cdn.com/v4/letter/e/c89c15/32.png) [@EHC](https://nextstrain.discourse.group/u/EHC)\
**Post date:** [February 12, 2023, 12:40pm UTC](https://nextstrain.discourse.group/t/ancestral-sequences/1332/1 "2023-02-12T12:40:15Z")

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Hi,  
I am new here. I would like to get the ancestral sequences for viruses in the online virus data in [nexstrain.org](http://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!

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**Author:** ![corneliusroemer](https://yyz1.discourse-cdn.com/flex031/user_avatar/nextstrain.discourse.group/corneliusroemer/32/175_2.png) [@corneliusroemer](https://nextstrain.discourse.group/u/corneliusroemer)\
**Post date:** [February 13, 2023, 11:02am UTC](https://nextstrain.discourse.group/t/ancestral-sequences/1332/2 "2023-02-13T11:02:46Z")

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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](https://docs.nextstrain.org/projects/augur/en/stable/usage/cli/ancestral.html)

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](https://github.com/nextstrain/monkeypox/blob/b54768ec17872eb0d898e29527785642f6b98c0d/workflow/snakemake_rules/core.smk#L271)

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**Author:** ![EHC](https://avatars.discourse-cdn.com/v4/letter/e/c89c15/32.png) [@EHC](https://nextstrain.discourse.group/u/EHC)\
**Post date:** [February 16, 2023, 1:51pm UTC](https://nextstrain.discourse.group/t/ancestral-sequences/1332/3 "2023-02-16T13:51:27Z")

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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?