Keyword(s):Phylogeny, Character State Phylogeny, Live Phylogeny, Parsimony, Algorithms.

Related
Ontology
Subjects/Areas/Topics:Bioinformatics
;
Biomedical Engineering
;
Pattern Recognition, Clustering and Classification

Abstract: In the character-based phylogeny reconstruction for n objects and m characters, the input is an nm-matrix
such that position i; j keeps the state of character j for the object i and the output is a binary rooted tree, where
the input objects are represented as leaves and each node v is labeled with a string of m symbols v1 : : :vm,
v j representing the state of character j, with minimal number of state changes along the edges of the tree,
considering all characters. This is called the Large Parsimony Problem. Live Phylogeny theory generalizes
the phylogeny theory by admitting living ancestors among the taxonomic objects. This theory suits cases
of fast-evolving species like virus, and phylogenies of non-biological objects like documents, images and
database records. In this paper we analyze problems related to most parsimonious tree using Live Phylogeny.
We introduce the Large Live Parsimony Problem (LLPP), prove that it is NP-complete and provide a branch
and bound solution. We also introduce and solve a simpler version, Small Live Parsimony Problem (SLPP),
which is used in the branch and bound.(More)

In the character-based phylogeny reconstruction for n objects and m characters, the input is an nm-matrix such that position i; j keeps the state of character j for the object i and the output is a binary rooted tree, where the input objects are represented as leaves and each node v is labeled with a string of m symbols v1 : : :vm, v j representing the state of character j, with minimal number of state changes along the edges of the tree, considering all characters. This is called the Large Parsimony Problem. Live Phylogeny theory generalizes the phylogeny theory by admitting living ancestors among the taxonomic objects. This theory suits cases of fast-evolving species like virus, and phylogenies of non-biological objects like documents, images and database records. In this paper we analyze problems related to most parsimonious tree using Live Phylogeny. We introduce the Large Live Parsimony Problem (LLPP), prove that it is NP-complete and provide a branch and bound solution. We also introduce and solve a simpler version, Small Live Parsimony Problem (SLPP), which is used in the branch and bound.

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Güths, R.; Telles, G.; Walter, M. and Almeida, N. (2017). A Branch and Bound for the Large Live Parsimony Problem. In Proceedings of the 10th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 3: BIOINFORMATICS, (BIOSTEC 2017) ISBN 978-989-758-214-1 ISSN 2184-4305, pages 184-189. DOI: 10.5220/0006219001840189

@conference{bioinformatics17, author={Rogério Güths. and Guilherme P. Telles. and Maria Emilia M. T. Walter. and Nalvo Almeida.}, title={A Branch and Bound for the Large Live Parsimony Problem}, booktitle={Proceedings of the 10th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 3: BIOINFORMATICS, (BIOSTEC 2017)}, year={2017}, pages={184-189}, publisher={SciTePress}, organization={INSTICC}, doi={10.5220/0006219001840189}, isbn={978-989-758-214-1}, issn={2184-4305}, }

TY - CONF

JO - Proceedings of the 10th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 3: BIOINFORMATICS, (BIOSTEC 2017) TI - A Branch and Bound for the Large Live Parsimony Problem SN - 978-989-758-214-1 IS - 2184-4305 AU - Güths, R. AU - Telles, G. AU - Walter, M. AU - Almeida, N. PY - 2017 SP - 184 EP - 189 DO - 10.5220/0006219001840189