Tn computes probability of unordered mutations instead of ordered mutations. A patch has been created that can help investigate the problem for revision 175.
We have checked that different order of mutations not on the same brunch does not lead to different gene trees, which was an assumption of the analysis. The bug description file has been updated on this.
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Patch for Tn.forwardEventProb
We have checked that different order of mutations not on the same brunch does not lead to different gene trees, which was an assumption of the analysis. The bug description file has been updated on this.