Attach likelihood object to tree params when processing yaml

[rmcar17]

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]

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

[YapengLang]

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]

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