### 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 language | English (US) |
---|---|

Pages (from-to) | 239-260 |

Number of pages | 22 |

Journal | Discrete Applied Mathematics |

Volume | 88 |

Issue number | 1-3 |

State | Published - Nov 9 1998 |

Externally published | Yes |

### Fingerprint

### Keywords

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

### ASJC Scopus subject areas

- Computational Theory and Mathematics
- Applied Mathematics
- Discrete Mathematics and Combinatorics
- Theoretical Computer Science

### Cite this

*Discrete Applied Mathematics*,

*88*(1-3), 239-260.

**Reconstructing a history of recombinations from a set of sequences.** / Kececioglu, John D; Gusfield, Dan.

Research output: Contribution to journal › Article

*Discrete Applied Mathematics*, vol. 88, no. 1-3, pp. 239-260.

}

TY - JOUR

T1 - Reconstructing a history of recombinations from a set of sequences

AU - Kececioglu, John D

AU - Gusfield, Dan

PY - 1998/11/9

Y1 - 1998/11/9

N2 - 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.

AB - 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.

KW - Bottleneck optimality

KW - Computational biology

KW - Directed hypergraphs

KW - Edit distance

KW - Evolutionary trees

KW - Recombination

UR - http://www.scopus.com/inward/record.url?scp=0039528958&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0039528958&partnerID=8YFLogxK

M3 - Article

AN - SCOPUS:0039528958

VL - 88

SP - 239

EP - 260

JO - Discrete Applied Mathematics

JF - Discrete Applied Mathematics

SN - 0166-218X

IS - 1-3

ER -