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pierrebarbera / epa-ng

Massively parallel phylogenetic placement of genetic sequences
GNU Affero General Public License v3.0
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How to convert the epa results (jplace) to the newick format? #46

Closed Bin-Ma closed 1 year ago

Bin-Ma commented 1 year ago

@stamatak I want to compare the placement with the reference tree. But I have no idea about how to convert the format to the newick? Looking forward to your reply!

lczech commented 1 year ago

Dear @Bin-Ma,

the gappa graft command can do that, see here: https://github.com/lczech/gappa/wiki/Subcommand:-graft

However, you should first read up on how to interpret that - as this is not a simple conversion. Phylogenetic Placement contains uncertainty of the placements, which is lost when turning the data into a Newick tree.

I'd recommend reading our review article for more information:

Metagenomic Analysis Using Phylogenetic Placement—A Review of the First Decade. Lucas Czech, Alexandros Stamatakis, Micah Dunthorn, and Pierre Barbera. Frontiers in Bioinformatics, 2022. https://doi.org/10.3389/fbinf.2022.871393

Hope that helps :-) Closing the issue now, but feel free to re-open should you have more questions!

Lucas

lczech commented 1 year ago

PS: Should you have more questions, you can also check out our google group: https://groups.google.com/forum/#!forum/phylogenetic-placement - which is the preferred place for questions like this.

Bin-Ma commented 1 year ago

Thanks for your reply. I will try it right now! @lczech