Reconstructing a history of recombinations from a set of sequences

John Kececioglu, Dan Gusfield

Research output: Contribution to journalArticle

36 Scopus citations

Abstract

One of the classic problems in computational biology is the reconstruction of evolutionary history. A recent trend in the area is to increase the explanatory power of the models that are considered by incorporating higher-order evolutionary events that more accurately reflect the mechanisms of mutation at the level of the chromosome. We take a step in this direction by considering the problem of reconstructing an evolutionary history for a set of genetic sequences that have evolved by recombination. Recombination is a non-tree-like event that produces a child sequence by crossing two parent sequences. We present polynomial-time algorithms for reconstructing a parsimonious history of such events for several models of recombination when all sequences, including those of ancestors, are present in the input. We also show that these models appear to be near the limit of what can be solved in polynomial time, in that several natural generalizations are NP-complete.

Original languageEnglish (US)
Pages (from-to)239-260
Number of pages22
JournalDiscrete Applied Mathematics
Volume88
Issue number1-3
DOIs
StatePublished - Nov 9 1998
Externally publishedYes

Keywords

  • Bottleneck optimality
  • Computational biology
  • Directed hypergraphs
  • Edit distance
  • Evolutionary trees
  • Recombination

ASJC Scopus subject areas

  • Discrete Mathematics and Combinatorics
  • Applied Mathematics

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