title: Recombination-filtered genomic datasets by information maximization.
abstract: With the increasing amount of DNA sequence data available from natural populations, new computational methods are needed to efficiently process raw sequences into formats that are applicable to a variety of analytical methods. One highly successful approach to inferring aspects of demographic history is grounded in coalescent theory. Many of these methods restrict themselves to perfectly tree-like genealogies (i.e. regions with no observed recombination), because theoretical difficulties prevent ready statistical evaluation of recombining regions. However, determining which recombination-filtered dataset to analyze from a larger recombination-rich genomic region is a non-trivial problem. Current applications primarily aim to quantify recombination rates (rather than produce optimal recombination-filtered blocks), require significant manual intervention, and are impractical for multiple genomic datasets in high-throughput, automated research environments. Here, we present a fast, simple and automatable command-line program that extracts optimal recombination-filtered blocks (no four-gamete violations) from recombination-rich genomic re-sequence data.
  
  
  BACKGROUND
  http://hammerlab.biosci.arizona.edu/software.html.
authors.affiliation: Arizona Research Laboratories-Biotechnology, University of Arizona, Tucson, AZ 85721, USA.
authors.forename: August E
authors.initials: AE
authors.lastname: Woerner
authors.forename: Murray P
authors.initials: MP
authors.lastname: Cox
authors.forename: Michael F
authors.initials: MF
authors.lastname: Hammer
mesh_terms: D000465:Algorithms; D001331:Automation; D019295:Computational Biology / Q000379:methods*; D004247:DNA / Q000737:chemistry; D030541:Databases, Genetic; D003710:Demography; D014644:Genetic Variation; D023281:Genomics / Q000379:methods; D006801:Humans; D008962:Models, Theoretical; D011381:Programming Languages; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D012984:Software
chemical_list: D004247:DNA