Together with Nikos Alachiotis (n.alachiotis at gmail dot com) we are building a webserver to run selective sweep analysis.
OmegaPlus analysis can be accessed from here.
SweeD analysis can be accessed from here.
When the analysis is complete, you will receive an email with the results. You can see a screen-shot below.
Fields with a * are compulsory. Some fields like “length” are needed only if you have ms format or MaCS format. You need to put your email since the results will be sent to you by email.
There are also advanced options ( click on ‘more options’). There you can specify additional parameters such as LD for OmegaPlus analysis, imputation options, balance options (-b) etc.
We have also implemented some R scripts that combine both of the tests. Please visit these pages for further information:
- Combine OmegaPlus and SweeD Thresholds from simulations
- Combine SweeD analysis with OmegaPlus analysis to detect common outliers
For comments please contact us at pavlidisp@gmail.com and n.alachiotis@gmail.com
In case you use these server tools please cite:
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SweeD: likelihood-based detection of selective sweeps in thousands of genomes. Pavlidis P, Živkovic D, Stamatakis A, Alachiotis N., Mol Biol Evol. 2013 Sep;30(9):2224-34. doi: 10.1093/molbev/mst112. Epub 2013 Jun 18.
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OmegaPlus: a scalable tool for rapid detection of selective sweeps in whole-genome datasets. Alachiotis N, Stamatakis A, Pavlidis P., Bioinformatics. 2012 Sep 1;28(17):2274-5. doi: 10.1093/bioinformatics/bts419. Epub 2012 Jul 3.