Inferring phylogenetic trees using answer set programming

DOI10.1007/s10817-007-9082-1zbMath1132.68676OpenAlexW1997780525MaRDI QIDQ2467563

Daniel Brooks, James W. Minett, Selim T. Erdoğan, Don Ringe, Esra Erdem

Publication date: 22 January 2008

Published in: Journal of Automated Reasoning (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1007/s10817-007-9082-1

zbMATH Keywords

PhylogenyAnswer set programmingCladistics

Mathematics Subject Classification ID

Related Items (9)

Finding similar/diverse solutions in answer set programming ⋮ Achievements in answer set programming ⋮ Optimizing phylogenetic supertrees using answer set programming ⋮ Disjunctive answer set solvers via templates ⋮ Stable-unstable semantics: Beyond NP with normal logic programs ⋮ Computing weighted solutions in ASP: representation-based method vs. search-based method ⋮ Unnamed Item ⋮ Unnamed Item ⋮ A Logic-Based Framework Leveraging Neural Networks for Studying the Evolution of Neurological Disorders

Uses Software

• Chaff
• PHYLIP
• PAUP*

Cites Work

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• The computational complexity of inferring rooted phylogenies by parsimony
• The Steiner problem in phylogeny is NP-complete
• The hardness of perfect phylogeny, feasible register assignment and other problems on thin colored graphs
• Answer set programming and plan generation
• Extending and implementing the stable model semantics
• Nested expressions in logic programs
• Weight constraints as nested expressions
• Tight logic programs
• Temporal phylogenetic networks and logic programming

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