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iqtree / piqtree2

a python library that exposes features from iqtree2 - efficient software for phylogenomic inference
GNU General Public License v2.0
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Attach likelihood object to tree params when processing yaml #27

Closed rmcar17 closed 1 month ago

rmcar17 commented 3 months ago

~The _process_tree_yaml function in _iq_wrappers.py is the place to do this!~

Now in src/piqtree2/iqtree/_tree.py: _process_tree_yaml

rmcar17 commented 2 months ago

Base frequencies are now included in the yaml output (#40, #47)

YapengLang commented 2 months ago

I've modified the _process_tree_yaml function to attach the rate and motif parameters to the cogent3 tree object.

These changes will now only apply to DNA models, excluding those in the Lie model list. I still need to explore those models' behaviour of the .yaml output further.

YapengLang commented 1 month ago

I will add tests for the branch length obtained from processing yaml.