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Treemmer : a tool to reduce large phylogenetic datasets with minimal loss of diversity

Menardo, Fabrizio and Loiseau, Chloé and Brites, Daniela and Coscolla, Mireia and Gygli, Sebastian M. and Rutaihwa, Liliana K. and Trauner, Andrej and Beisel, Christian and Borrell, Sonia and Gagneux, Sebastien. (2018) Treemmer : a tool to reduce large phylogenetic datasets with minimal loss of diversity. BMC bioinformatics, 19 (1). p. 164.

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Abstract

Large sequence datasets are difficult to visualize and handle. Additionally, they often do not represent a random subset of the natural diversity, but the result of uncoordinated and convenience sampling. Consequently, they can suffer from redundancy and sampling biases.; Here we present Treemmer, a simple tool to evaluate the redundancy of phylogenetic trees and reduce their complexity by eliminating leaves that contribute the least to the tree diversity.; Treemmer can reduce the size of datasets with different phylogenetic structures and levels of redundancy while maintaining a sub-sample that is representative of the original diversity. Additionally, it is possible to fine-tune the behavior of Treemmer including any kind of meta-information, making Treemmer particularly useful for empirical studies.
Faculties and Departments:09 Associated Institutions > Swiss Tropical and Public Health Institute (Swiss TPH)
09 Associated Institutions > Swiss Tropical and Public Health Institute (Swiss TPH) > Department of Medical Parasitology and Infection Biology > Tuberculosis Research (Gagneux)
UniBasel Contributors:Menardo, Fabrizio and Loiseau, Chloé Marie and Brites, Daniela and Coscollá Devís, Mireia and Gygli, Sebastian and Rutaihwa, Liliana and Trauner, Andrej and Borrell Farnov, Sonia and Gagneux, Sebastien
Item Type:Article, refereed
Article Subtype:Research Article
Publisher:BioMed Central
ISSN:1471-2105
Note:Publication type according to Uni Basel Research Database: Journal article
Language:English
Identification Number:
Last Modified:01 Mar 2019 13:42
Deposited On:01 Mar 2019 13:42

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