Getting started with DFE for MusMus #1556
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add line to init importing dfe fix neutral,non-neutral props. try shorter dfe model name
petrelharp
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I've rebased this; we'll see what needs to be done? |
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Okay - looking at the paper, I've got a few questions: should we be (also?) implementing a DFE with positive selection? And, should we be worried this paper from 2021 is still a preprint? |
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@petrelharp I think we could implement a couple of different scenarios, I just wanted to make sure this simplest scenario, or at least a scenario that is present for a few other species in the catalog, passed spec before trying others. An alternative citation that could be included as well because it includes some of the same/similar simulations is here. |
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Sounds good. If the intention is to implement more than one from the same paper, perhaps the name needs additional information? Like I don't know maybe I checked with Tom Booker, btw, who says we're good to use this - there's no issue with this part of the analysis. |
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Okay, I think this looks good! Mind opening a QC issue, @peterdfields? |
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@petrelharp Sure, I can open the QC issue. Regarding the other scenarios, I should open another branch for these? I definitely figured we were on strong footing for the parameter values/details given Tom had worked them up :) |
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Great, thanks! And yes - if you'd like to add more, open a new PR. (Should be easy now?) |
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I started this in #1649, so it wouldn't be forgotten - could you provide more info there, please? |
@igronau Just getting the pull started for MusMus. Here I've implemented the base DFE for CDS from here. Note that there is also a DFE for CNE and UTR type genomic sequence but I wanted to make sure the CDS is parameterized correctly first.