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venelin/PCMBase: Before disentangling tree-parts from model regimes

Venelin Mitov; Georgios Asimomitis; krzbar

This is the latest version of the package using the old concept of model regimes, where a regime was mapped to monophyletic or polyphyletic group of nodes on the tree.

In the versions to follow, the concept of a regime will be split into two related concepts: In the context of a tree, we will use the word 'part' to denote a monophyletic or a paraphyletic group of nodes. In the context of a model, we will use the word 'regime' to denote an instance of the model parameters. A suitable synonym for 'regime' would thus be 'color'. It is possible for several parts on a tree to have the same color, i.e. the same model regime.

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