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adamallo / SimPhy

SimPhy: A comprehensive simulator of gene family evolution
GNU General Public License v2.0
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Invalid gene loss rate #9

Closed BenoitMorel closed 4 years ago

BenoitMorel commented 4 years ago

Hi Adamallo,

Thanks a lot for your great simulator!

I have a question regarding the loss and duplication rates: you forbid the loss rate to be lower than the duplication rate (https://github.com/adamallo/SimPhy/blob/master/src/main.c#L3637)

Is it because it would almost certainly imply that all gene lineages would go extinct? What if I also add transfers? (for instance, if I want no gene duplication, but gene transfer and loss)

Benoit

adamallo commented 4 years ago

The current version of SimPhy only implements horizontal gene transfer/lateral gene transfer that replaces a pre-existing gene copy (locus tree branch). Therefore, the transfer rate does not modify the expected number of locus-tree leaves.

In any case, it is true that the current error forcing duplication rate to be >= loss rate is too restrictive, since it may make sense to simulate under these conditions. In fact, this issue has been reported before (see https://groups.google.com/forum/#!topic/simphy/99Yu_Failes ). I plan to relax this strict control of the input simulation parameter values in the main branch of SimPhy. In the meantime, please, try the flexiblesim branch of the repository. This allows to relax this condition when using the argument "-f 1".

Thanks,

DM

BenoitMorel commented 4 years ago

Great now everything makes sense. Thanks a lot for your explanations!