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The HS-MSC ILP does not enforce that individuals must have one parent of each sex and both partition distance and variation of information are ill-defined when the result is not a true partitioning.
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The number of bins here is 3.
Huelsenbeck and Andolfatto [22] measured accuracy as the average distance of the sampled partitions to the true partition using a metric described by Gusfield [37], the partition distance.
The left and right correspond to the true partition being A | BCD or AB | CD, respectively.
If two data points belong to the same true partition of, they are called connected.
Finally, the third partitioning strategy used the true partition defined by the breakpoints where the true topology changed.
Accuracy was evaluated on the simulated datasets using the ARI calculated between the output cluster partitions and the true partitions.
As a result, the chance that the credible set contains only the true partition is slightly higher.
The tree reconstruction from the true partition with known breakpoints actually revealed a substantial amount of systematic error from MrBayes.
On MDL partitions or on the true partition, the informative prior α = 1 provided little or no increase in accuracy over the consensus prior.
Compared with the accuracy obtained with the true partition, MDL partitioning provides an almost optimal accuracy in the presence of HGT.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com