Dataset Information

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

ABSTRACT: BACKGROUND: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. RESULTS: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. CONCLUSIONS: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.

SUBMITTER: Menardo F

PROVIDER: S-EPMC5930393 | biostudies-literature | 2018 May

REPOSITORIES: biostudies-literature

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

Menardo Fabrizio F Loiseau Chloé C Brites Daniela D Coscolla Mireia M Gygli Sebastian M SM Rutaihwa Liliana K LK Trauner Andrej A Beisel Christian C Borrell Sonia S Gagneux Sebastien S

BMC bioinformatics 20180502 1

<h4>Background</h4>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.<h4>Results</h4>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.<h4>Con ...[more]

PMID: 29716518

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Dataset Information

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

Publications

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

Similar Datasets

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