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lmaurits / BEASTling

A linguistics-focussed command line tool for generating BEAST XML files.
BSD 2-Clause "Simplified" License
20 stars 6 forks source link

Tutorial: Generate trees from actual sampled output #106

Open Anaphory opened 7 years ago

Anaphory commented 7 years ago

The tutorial contains figures depicting trees.

We don't have the tools for it yet, but in the long run, it might become useful to set up something that will generate these figures from the directory scriptdoctest runs the example code in. While this will never become a clean unittest, this would at least give us a visual confirmation for how the full loop from beastling configuration file to output tree works.

[Milestone: NOT 1.2]

lmaurits commented 7 years ago

In a fantasy land where I had the time to dedicate to it, my next big project alongside BEASTling and phyltr would be a 100% scriptable tree plotting tool. There is a sore need for this. I like ETE in general for mucking around with trees in Python, but I don't consider it possible to get nice publication quality figures out of it (at least not without an insane amount of fiddling). I don't think DendroPy is much better, either. FigTree can produce very nice looking, information-rich figures, but only with hours of manual pointing and clicking which have to be painstakingly repeated for each new tree.

Anaphory commented 7 years ago

Some of the ete3 example trees look quite nice from a distance, what are your issues with the toolkit?

Is the code you used to generate the trees in the tutorial available somewhere?