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Analyses

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Iakov Davydov edited this page Sep 12, 2016 · 2 revisions

HyPhy

  1. ~/hyphy/hyphy-2.2.6/build/HYPHYMP ~/hyphy/hyphy-2.2.6/res/TemplateBatchFiles/Q.uickSelectionDetection.bf
  2. (1):[Universal] Universal code (note: in future we might need to support other genetic codes)
  3. full path to the alignment in phylip format
  4. (1):[Default] Use HKY85 and MG94xHKY85.
  5. (4):[Estimate + CI] Estimate dN/dS and a 95% confidence interval from data (slower).
  6. (11):[MEME] Mixed effects model of evolution to search for evidence of episodic selection at indvidual sites [EXPERIMENTAL, March 2011]
  7. Significance level 0.05

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