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As far as I know, you can run a command in the bar button to remove animation node trees. But I would like to automate this with another script, for rigging purposes.

This doesn't work:

bpy.ops.an.remove_node_tree("nodetreename")

As far as I know, there is an error Invoking the right window?

Any clue how to script this?

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You should be able to do it like so:

bpy.data.node_groups.remove(bpy.data.node_groups["tree name"])
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