loss rate > duplication rate

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Qiuyi Li

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Apr 25, 2021, 6:02:59 AM4/25/21

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Hi all,

Just one more question to add here:

Can we possibly have loss rate > duplication rate in SimPhy?

I know this may cause the "all lost" scenario, but one the other hand we noticed that the number of genes still increases through time even though we have dup_rate=loss_rate. I would like to see how much should I increase the loss rate so that the number of genes will stay stable.

Currently SimPhy does not allow the user to have loss_rate > duplicate but I suppose this should be easy to fix?

Qiuyi

Diego M.

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Apr 26, 2021, 12:05:42 PM4/26/21

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Dear Qiuyi,

There is a Github branch in SimPhy's repository that deals with this issue. The name is "flexiblesim." You can find more information on how to use this version of SimPhy on this GitHub issue "https://github.com/adamallo/SimPhy/issues/9". Qiuyi, let me know if you have any problems compiling this version of the code. I am happy to provide a compiled version if you have any.