### Sammanfattning

trees with possibly conflicting information into a single tree that has all the

leaves of the source trees as its leaves and the relationships between the

leaves are as consistent with the source trees as possible. This leads to an

optimization problem that is computationally challenging and typically

heuristic methods, such as matrix representation with parsimony (MRP), are

used. In this paper we consider the use of answer set programming to solve the

supertree construction problem in terms of two alternative encodings. The first

is based on an existing encoding of trees using substructures known as

quartets, while the other novel encoding captures the relationships present in

trees through direct projections. We use these encodings to compute a

genus-level supertree for the family of cats (Felidae). Furthermore, we compare

our results to recent supertrees obtained by the MRP method.

Originalspråk | engelska |
---|---|

Tidskrift | Theory and Practice of Logic Programming |

Volym | 15 |

Utgåva | 4-5 |

Sidor (från-till) | 604-619 |

Antal sidor | 16 |

ISSN | 1471-0684 |

DOI | |

Status | Publicerad - jul 2015 |

MoE-publikationstyp | A1 Tidskriftsartikel-refererad |

### Vetenskapsgrenar

- 1171 Geovetenskaper

### Citera det här

*Theory and Practice of Logic Programming*,

*15*(4-5), 604-619. https://doi.org/10.1017/S1471068415000265

}

*Theory and Practice of Logic Programming*, vol. 15, nr. 4-5, s. 604-619. https://doi.org/10.1017/S1471068415000265

**Optimizing Phylogenetic Supertrees Using Answer Set Programming.** / Koponen, Laura; Oikarinen, Emilia; Janhunen, Tomi; Säilä-Corfe, Laura Kristina.

Forskningsoutput: Tidskriftsbidrag › Artikel › Vetenskaplig › Peer review

TY - JOUR

T1 - Optimizing Phylogenetic Supertrees Using Answer Set Programming

AU - Koponen, Laura

AU - Oikarinen, Emilia

AU - Janhunen, Tomi

AU - Säilä-Corfe, Laura Kristina

PY - 2015/7

Y1 - 2015/7

N2 - The supertree construction problem is about combining several phylogenetictrees with possibly conflicting information into a single tree that has all theleaves of the source trees as its leaves and the relationships between theleaves are as consistent with the source trees as possible. This leads to anoptimization problem that is computationally challenging and typicallyheuristic methods, such as matrix representation with parsimony (MRP), areused. In this paper we consider the use of answer set programming to solve thesupertree construction problem in terms of two alternative encodings. The firstis based on an existing encoding of trees using substructures known asquartets, while the other novel encoding captures the relationships present intrees through direct projections. We use these encodings to compute agenus-level supertree for the family of cats (Felidae). Furthermore, we compareour results to recent supertrees obtained by the MRP method.

AB - The supertree construction problem is about combining several phylogenetictrees with possibly conflicting information into a single tree that has all theleaves of the source trees as its leaves and the relationships between theleaves are as consistent with the source trees as possible. This leads to anoptimization problem that is computationally challenging and typicallyheuristic methods, such as matrix representation with parsimony (MRP), areused. In this paper we consider the use of answer set programming to solve thesupertree construction problem in terms of two alternative encodings. The firstis based on an existing encoding of trees using substructures known asquartets, while the other novel encoding captures the relationships present intrees through direct projections. We use these encodings to compute agenus-level supertree for the family of cats (Felidae). Furthermore, we compareour results to recent supertrees obtained by the MRP method.

KW - 1171 Geosciences

U2 - 10.1017/S1471068415000265

DO - 10.1017/S1471068415000265

M3 - Article

VL - 15

SP - 604

EP - 619

JO - Theory and Practice of Logic Programming

JF - Theory and Practice of Logic Programming

SN - 1471-0684

IS - 4-5

ER -