title: hotspot: software to support sperm-typing for investigating recombination hotspots.
abstract: In many organisms, including humans, recombination clusters within recombination hotspots. The standard method for de novo detection of recombinants at hotspots is sperm typing. This relies on allele-specific PCR at single nucleotide polymorphisms. Designing allele-specific primers by hand is time-consuming. We have therefore written a package to support hotspot detection and analysis.
  
  
  
  hotspot consists of four programs: asp looks up SNPs and designs allele-specific primers; aso constructs allele-specific oligos for mapping recombinants; xov implements a maximum-likelihood method for estimating the crossover rate; six, finally, simulates typing data.
  
  
  
  hotspot is written in C. Sources are freely available under the GNU General Public License from http://github.com/evolbioinf/hotspot/
  
  
  
  haubold@evolbio.mpg.de
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Biology, Plön, Germany.
authors.forename: Linda
authors.initials: L
authors.lastname: Odenthal-Hesse
authors.affiliation: Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Biology, Plön, Germany.
authors.forename: Julien Y
authors.initials: JY
authors.lastname: Dutheil
authors.affiliation: Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Biology, Plön, Germany.
authors.forename: Fabian
authors.initials: F
authors.lastname: Klötzl
authors.affiliation: Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Biology, Plön, Germany.
authors.forename: Bernhard
authors.initials: B
authors.lastname: Haubold
mesh_terms: D000483:Alleles; D006801:Humans; D016013:Likelihood Functions; D008297:Male; D011995:Recombination, Genetic; D012984:Software; D013094:Spermatozoa