Linkage Disequilibrium as a Signature of Selective Sweeps

No abstract is available for this paper.

• Publication year

  2004

• Venue

  Genetics

• Publication date

  2004-07-01

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1534/GENETICS.103.025387PMID 15280259PMCID PMC1470945
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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• Estimating the distribution of selection coefficients from phylogenetic data with applications to mitochondrial and viral DNA.

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