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The simplest probability models for character mutation are continuous time Markov chains with finite state space U. We introduce three such models employed in this study next.
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In our study, however, the simplest model for character evolution was favored in the model exploration for a single tree topology.
The model consists of a number of parameters, the most basic being: a tree topology, a set of branch lengths and an evolutionary model for character change.
Second, we tested for a difference in rates by examining the results for our gamma model for character evolution (see above).
When the model for character evolution on a single tree is overly simple compared to the actual process of character evolution, the Bayes factor test for different trees is thought to produce spurious positive results due to model misspecification.
The degree of "tree-likeness" in data under a parsimony model for character change was measured by consistency index (CI) and retention index (RI).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com