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 hi...

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Bibliographic Details
Published in:Bioinformatics Vol. 36; no. 10; pp. 3263 - 3265
Main Authors: Czech, Lucas, Barbera, Pierre, Stamatakis, Alexandros
Format: Journal Article
Language:English
Published: England Oxford University Press 01.05.2020
Subjects:
Applications Notes
Gene Library
Libraries
Phylogeny
Software
ISSN:1367-4803, 1367-4811, 1460-2059, 1367-4811
Online Access:Get full text
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Summary: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.
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ISSN:1367-4803
1367-4811
1460-2059
1367-4811
DOI:10.1093/bioinformatics/btaa070