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A tool to detect single nucleotide polymorphism (SNP) and to reconstruct haplotypes of a diploid organism, i.e., it can identify SNPs originating from each parent. The linkSNPs algorithm requires, on average, five heterozygous sites per kilobase of sequence.


Genetics; DNA polymorphism


  • Operation: SNP detection; haplotype mapping
  • Software interface: Command-line user interface
  • Language: Perl
  • Operating system: Microsoft Windows, Mac OS X, Linux
  • License: Not stated
  • Cost: Free
  • Version name: 1.2
  • Maturity: Stable
  • Credit: -
  • Contact: innan_hideki _at_ | eriko.sasaki _at_
  • Collection: -


Sasaki E, Sugino RP, Innan H "The linkage method: a novel approach for SNP detection and haplotype reconstruction from a single diploid individual using next-generation sequence data." Mol Biol Evol. 2013 Sep;30(9):2187-96. 31.
PMID: 23728796

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