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ekirving / mesoneo_paper

Source code from the paper: "The Selection Landscape and Genetic Legacy of Ancient Eurasians" (2024) Nature
https://doi.org/10.1038/s41586-023-06705-1
MIT License
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Running 'run_ancient.sh' #2

Closed KishoreChopra closed 5 months ago

KishoreChopra commented 5 months ago

Hi, if I want to estimate allele frequency trajectories using only aDNA, can I only use the file under "ancestral_paths_v3:"? Do I need to include modern groups in my file? Are there any other considerations or points to keep in mind?

ekirving commented 5 months ago

If all you want to do is infer frequency trajectories using only aDNA then you don't need my pipeline, and you would be better off using CLUES directly. See https://github.com/standard-aaron/clues/wiki/Command-line-options-for-CLUES for documentation.

KishoreChopra commented 5 months ago

Thank you very much !!!