arvestad / jprime

Probabilistic Inference of Molecular Evolution
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GenPhyloData does not count lost genes in pruned trees #22

Open arvestad opened 7 years ago

arvestad commented 7 years ago

The number of losses is always set to zero when GuestTreeGen is providing the .pruned.info file. The .unpruned version of the file is displaying the actual number of losses, but that is of course an overestimate of what can be seen in the pruned case.

I have checked this with Notung. See attached files for example data.

example.zip