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Add "Simplify phylogeny" button to simplify trees (especially Open Tree of Life induced subtree) #241

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gaurav opened this issue Mar 29, 2022 · 1 comment
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programming only No discussion necessary; just pure programming needed

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@gaurav
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gaurav commented Mar 29, 2022

Open Tree of Life induced subtrees (as added by #40) include a large number of internal nodes that only have a single child, which can make visualizing the phylogeny complicated. However, we can't just delete all such internal nodes when importing a phylogeny from the Open Tree of Life as they might be useful -- for example, one of these nodes might be a specifier. As far as I know, there's no setting on the Open Tree /tree_of_life/induced_subtree API call to control this.

We could add a "Remove internal nodes with only a single child" button to the phylogeny view, which would ignore internal nodes that are used as specifiers. We could also go further and add a "Simplify phylogeny" button that removes all phylogeny nodes except specifiers and their parents. Alternatively, we could decide that this is too much complexity for Klados and leave it up to the user to use an external tool to clean up their phylogenies in any way they choose.

@gaurav gaurav added the discussion needed Discussion is needed before this issue can be closed label Mar 29, 2022
@gaurav gaurav added this to the Klados v1.0 milestone Mar 29, 2022
@hlapp
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hlapp commented Apr 8, 2022

It seems reasonable and also useful to a Simplify phylogeny option that removes internal nodes that only have one child and whose label does not match any of the specifiers.

I think that's neither of the alternatives you present but an amalgamation of them. Does this make sense, though?

@gaurav gaurav removed the discussion needed Discussion is needed before this issue can be closed label Aug 24, 2022
@gaurav gaurav changed the title Decide on how to clean up Open Tree of Life induced subtree Add "Simplify phylogeny" button to simplify trees (especially Open Tree of Life induced subtree) Nov 2, 2022
@gaurav gaurav added the programming only No discussion necessary; just pure programming needed label May 24, 2023
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