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Newick files without lengths should not be coerced to distances of 1 #440

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gaurav opened this issue Aug 30, 2023 · 1 comment
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@gaurav
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gaurav commented Aug 30, 2023

In previous versions of phylotree.js, a Newick file without lengths was read as a Newick file without length. In the current version of phylotree.js, a Newick file without length is assumed to have a length of 1 at each edge. This is annoying in two ways:

  1. Phylogenies are incorrectly drawn to appear as if the length is 1, which could be misleading.
  2. It makes it harder for phylotree.js to be used in a phylogeny editor (as described in getNewick() returns unquoted Newick strings #438 (comment)), since the Newick produced by a Phylotree instance isn't identical to the Newick passed to it.

Would it be possible to have an option for turning this off?

@gaurav gaurav changed the title Newick files without distances should not be coerced to distances of 1 Newick files without lengths should not be coerced to distances of 1 Aug 30, 2023
@stevenweaver
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Dear @gaurav,

Yes, I think having an option to turn that off is a good idea.

Best,
Steven

@stevenweaver stevenweaver self-assigned this Sep 7, 2023
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