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jeetsukumaran / DendroPy

A Python library for phylogenetic scripting, simulation, data processing and manipulation.
https://pypi.org/project/DendroPy/.
BSD 3-Clause "New" or "Revised" License
210 stars 61 forks source link

Option to give leaf nodes in polytomies a default order in Tree.ladderize. #186

Closed davipatti closed 3 months ago

davipatti commented 7 months ago

I added this option to reduce unnecessary cross overs in tangle plots of trees that have polytomies.

mmore500 commented 7 months ago

@davipatti thank you for the contribution! I’m hoping to follow up and review it this upcoming week 👍

mmore500 commented 6 months ago

@davipatti — do you think similar functionality could be achieved by sorting the tip polytomies before the ladderization process?

davipatti commented 4 months ago

@davipatti — do you think similar functionality could be achieved by sorting the tip polytomies before the ladderization process?

@mmore500 sorry for being slow to reply. I guess that could also work. This seemed like a more explicit approach.

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mmore500 commented 3 months ago

@davipatti I ended up pushing to the wrong branch by accident, so this pull request ended up closing sooner than I intended without being able to run suggestions by.

I implemented a "reorder" function that, by default, sorts by label. I added a note to the documentation suggesting that ladderization sort is stable, so to control order within ladderization, call reorder before ladderizing. Let me know if this covers your use case.