Transition Model Language

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Overview

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.

Analysis of current needs

(what do we have now? what is missing? what challenges are coming up?)

Goals for the working group

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Strategy for achieving goal

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