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Genesis and Gappa: processing, analyzing and visualizing phylogenetic (placement) data.

ABSTRACT: SUMMARY:We present genesis, a library for working with phylogenetic data, and gappa, an accompanying command-line tool for conducting typical analyses on such data. The tools target phylogenetic trees and phylogenetic placements, sequences, taxonomies and other relevant data types, offer high-level simplicity as well as low-level customizability, and are computationally efficient, well-tested and field-proven. AVAILABILITY AND IMPLEMENTATION:Both genesis and gappa are written in modern C++11, and are freely available under GPLv3 at http://github.com/lczech/genesis and http://github.com/lczech/gappa. SUPPLEMENTARY INFORMATION:Supplementary data are available at Bioinformatics online.

SUBMITTER: Czech L

PROVIDER: S-EPMC7214027 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature

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Genesis and Gappa: processing, analyzing and visualizing phylogenetic (placement) data.

Czech Lucas L Barbera Pierre P Stamatakis Alexandros A

Bioinformatics (Oxford, England) 20200501 10

<h4>Summary</h4>We present genesis, a library for working with phylogenetic data, and gappa, an accompanying command-line tool for conducting typical analyses on such data. The tools target phylogenetic trees and phylogenetic placements, sequences, taxonomies and other relevant data types, offer high-level simplicity as well as low-level customizability, and are computationally efficient, well-tested and field-proven.<h4>Availability and implementation</h4>Both genesis and gappa are written in m ...[more]

PMID: 32016344

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Project description:[This corrects the article DOI: 10.1371/journal.pone.0217050.].

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