alder

ALDER is a software tool to infer admixture proportions, dates, and phylogenetic relationships based on linkage disequilibrium (LD) patterns in Human populations. The alder algorithm uses weighted statistics to produce an interpretable amplitude of the weighte LD curve, computes unbiased weighted LD using the test population itself, statistical tests for admixture, the affine term using inter-chromosome SNP pairs, and uses a fast Fourier transform (FFT) algorithm to decrease the computation time.

Topic

Population genetics

Detail

  • Operation: Phylogenetic tree analysis

  • Software interface: Command-line user interface

  • Language: C

  • License: The MIT licence

  • Cost: Free

  • Version name: 1.0.3

  • Credit: National Science Foundation (NSF), National Institutes of Health (NIH), the Simons Foundation.

  • Input: -

  • Output: -

  • Contact: Po-Ru Loh loh@hsph.harvard.edu, David Reich reich@genetics.med.harvard.edu, Bonnie Berger bab@mit.edu

  • Collection: -

  • Maturity: -

Publications

  • Inferring admixture histories of human populations using linkage disequilibrium.
  • Loh PR, Lipson M, Patterson N, Moorjani P, Pickrell JK, Reich D, Berger B. Inferring admixture histories of human populations using linkage disequilibrium. Genetics. 2013 Apr;193(4):1233-54. doi: 10.1534/genetics.112.147330. Epub 2013 Feb 14. PMID: 23410830; PMCID: PMC3606100.
  • https://doi.org/10.1534/genetics.112.147330
  • PMID: 23410830
  • PMC: PMC3606100

Download and documentation

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