Transition Model Language

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For analyses that use parsimony, the ASSUMPTIONS block of a NEXUS file provides a flexible way to describe rules, including costs or weights for each type of transition.  However, evolutionary analyses today typically use a model of state-transition probabilities parameterized via some (more or less) mechanistic scheme that introduces terms other than observed states (e.g., hidden states like a rate parameter for a site or an equilibrium GC content).  Individual programs such as MrBayes or HyPhy have their own languages for describing these models.  A common language would be highly useful for creating flexible pipelines and for comparative evaluation of methods.

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