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Demographic history with dadi

IC Ira Cooke

Last updated date: Dec 4, 2020 Views: 859 Forks: 0

original An abbreviated version of this protocol was published in Science Advances in Nov, 2020
Genomic signatures in the coral holobiont reveal host adaptations driven by Holocene climate change and reef specific symbionts
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Dear Joana, 


Please see our extended supp info http://github.com/iracooke/atenuis_wgs_pub

Since we performed our analysis there have been several developments.  dadi has been updated and is now much faster.  A new package called moments provides an alternative numerical engine for dadi.  There is also a new package called gadma for automatic searching of the model space, and there is also this repo https://github.com/z0on/AFS-analysis-with-moments which provides an exhaustive set of models for two population inference. 


Best wishes

Ira



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How to cite：
Readers should cite both the Bio-protocol preprint and the original research article where this protocol was used:
  1. Cooke, I(2020). Demographic history with dadi. Bio-protocol Preprint. bio-protocol.org/prep681.
  2. Cooke, I., Ying, H., Forêt, S., Bongaerts, P., Strugnell, J. M., Simakov, O., Zhang, J., Field, M. A., Rodriguez-Lanetty, M., Bell, S. C., Bourne, D. G., Oppen, M. J. V., Ragan, M. A. and Miller, D. J.(2020). Genomic signatures in the coral holobiont reveal host adaptations driven by Holocene climate change and reef specific symbionts . Science Advances 6(48). DOI: 10.1126/sciadv.abc6318

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