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Do we support annotations in Newick? #324

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gaurav opened this issue Feb 28, 2024 · 1 comment
Open

Do we support annotations in Newick? #324

gaurav opened this issue Feb 28, 2024 · 1 comment

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@gaurav
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gaurav commented Feb 28, 2024

For now we should ignore annotations.

@gaurav gaurav added this to the Klados v1.0 milestone Feb 28, 2024
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gaurav commented Feb 26, 2025

It looks like phylotree.js doesn't support Nexus comments like we're used to (e.g. [&phyloref:actual="#Alligatorinae",phyloref:actualLabel="Alligatorinae"]), but it does support "tags", using curly brackets (the example they provided is (a,(b{TAG},(c{TAG},d{ANOTHERTAG}))) as in their Newick parsing code.

So:

  1. We can't read Newick strings produced by our Nexus, but that's fine -- we don't support Nexus anyway.
  2. We can't read Newick strings with Nexus comments from other sources, but I don't think people would expect that.
  3. We don't do anything useful with the "tags" read by Newick.

I think all of that is fine for Klados v1.0. Should we close this issue?

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