Keyword(s):Evolution, Phylogeny, Live Phylogeny, Neighbor-joining.

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

Abstract: The Distance-Based Live Phylogeny Problem generalizes the well-known Distance-Based Phylogeny Problem
by admitting live ancestors among the taxonomic objects. This problem suites in cases of fast-evolving species
that co-exist and are ancestors/descendants at the same time, like viruses, and non-biological objects like documents,
images and database records. For n objects, the input is an nn-matrix where position i; j represents
the evolutionary distance between the objects i; j. Output is an unrooted, weighted tree where the objects may
be represented either as leaves or as internal nodes, and the distances between pairs of objects in the tree are
equal to the distances in the corresponding positions in the matrix. When the matrix is additive, it is easy
to find such a tree. In this work we prove that the problem of minimizing the residual differences between
path-lengths along the tree and pairwise distances in the matrix is computationally hard when the matrix is
not additive. We propose a heuristic, called Live-NJ, to solve the problem that reconstructs the evolutionary
history based on the well-known Neighbor-Joining algorithm. Results shown that Live-NJ performs better
when compared to NJ, being a promising approach to solve the Distance-Based Live Phylogeny Problem.(More)

The Distance-Based Live Phylogeny Problem generalizes the well-known Distance-Based Phylogeny Problem by admitting live ancestors among the taxonomic objects. This problem suites in cases of fast-evolving species that co-exist and are ancestors/descendants at the same time, like viruses, and non-biological objects like documents, images and database records. For n objects, the input is an nn-matrix where position i; j represents the evolutionary distance between the objects i; j. Output is an unrooted, weighted tree where the objects may be represented either as leaves or as internal nodes, and the distances between pairs of objects in the tree are equal to the distances in the corresponding positions in the matrix. When the matrix is additive, it is easy to find such a tree. In this work we prove that the problem of minimizing the residual differences between path-lengths along the tree and pairwise distances in the matrix is computationally hard when the matrix is not additive. We propose a heuristic, called Live-NJ, to solve the problem that reconstructs the evolutionary history based on the well-known Neighbor-Joining algorithm. Results shown that Live-NJ performs better when compared to NJ, being a promising approach to solve the Distance-Based Live Phylogeny Problem.

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Araújo, G.; Telles, G.; M. T. Walter, M. and Almeida, N. (2017). Distance-based Live Phylogeny.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, pages 196-201. DOI: 10.5220/0006224501960201

@conference{bioinformatics17, author={Graziela S. Araújo. and Guilherme P. Telles. and Maria Emília M. T. Walter. and Nalvo F. Almeida.}, title={Distance-based Live Phylogeny}, booktitle={Proceedings of the 10th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 3: BIOINFORMATICS, (BIOSTEC 2017)}, year={2017}, pages={196-201}, publisher={SciTePress}, organization={INSTICC}, doi={10.5220/0006224501960201}, isbn={978-989-758-214-1}, }

TY - CONF

JO - Proceedings of the 10th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 3: BIOINFORMATICS, (BIOSTEC 2017) TI - Distance-based Live Phylogeny SN - 978-989-758-214-1 AU - Araújo, G. AU - Telles, G. AU - M. T. Walter, M. AU - Almeida, N. PY - 2017 SP - 196 EP - 201 DO - 10.5220/0006224501960201