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gaynorr / AlphaSimR

R package for breeding program simulations
https://gaynorr.github.io/AlphaSimR/
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Implement tree sequence #126

Open gregorgorjanc opened 1 year ago

gregorgorjanc commented 1 year ago

This is a big one and a project on its own, but here are some initial ideas

gregorgorjanc commented 9 months ago

Peter Ralph directed me to this implementation doc for SLiM https://github.com/MesserLab/SLiM/blob/master/treerec/implementation.md

gaynorr commented 9 months ago

Need to change recombination tracking in AlphaSimR to keep track of all recombinations and not just observed recombinations. This can be accomplished by not processing recombination output from findBivalent and only processing the output within bivalent for the purposes of copying data.

The full history can then be fowarded along to recombination tracking. Processing will be needed in the current recombination history list, because it depends on this data being processed. Perhaps we need to recombination histories, or some adjustments to the current IBD tracking to process as needed.

gaynorr commented 9 months ago

Mutations need to be tracked for tree sequences. This can be added to SimParam.

gaynorr commented 8 months ago

https://www.slendr.net/articles/vignette-05-tree-sequences.html

Look at this article for an example implementation in R.