Refine without an alignment


I have a phylogenetic tree along with metadata (dates, locations, etc), but do not have the underlying sequences.

Treetime does not require an alignment, and I can run it for my example. However, running augur refine I get “ERROR: alignment is required for ancestral reconstruction or timetree inference”… which I don’t think is quite true.

It’s a bit of a pain to reformat treetime output for subsequent augur stages, so it would be nice to run this in augur itself.

Any help would be appreciated!

Hi @avoorman

I am not sure what final output you are looking for. But treetime produces an auspice.json output (since version 0.10.0) that you can view in You can then drag the metadata onto the tree display and it should include that as coloring.

if you want to run additional augur steps, some elements of this script might be useful

to generate the output of refine.


Thank you! I upgraded my treetime and now see the auspice json; the branch length code looks useful as well. As my next step was to infer ancestral traits, it seems like I could just do it all with treetime.

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