Recombination-filtered genomic datasets by information maximization

August E. Woerner, Murray P. Cox, Michael F. Hammer

Research output: Contribution to journalArticle

159 Scopus citations

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.

Original languageEnglish
Pages (from-to)1851-1853
Number of pages3
JournalBioinformatics
Volume23
Issue number14
DOIs
StatePublished - 15 Jul 2007

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