RapGreen, an interactive software and web package to explore and analyze phylogenetic trees

Jean-François Dufayard (1, 2, 3) , Stéphanie Bocs (2, 3, 1) , Valentin Guignon (4, 3) , Delphine Larivière (1, 3) , Alexandra Louis (5) , Nicolas Oubda (3, 1) , Mathieu Rouard (3) , Manuel Ruiz (2, 3, 1) , Frédéric F. de Lamotte (3, 1)

1 UMR AGAP - Amélioration génétique et adaptation des plantes méditerranéennes et tropicales
2 Cirad-BIOS - Département Systèmes Biologiques
3 IFB-CORE - Institut Français de Bioinformatique
4 Alliance - Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT) [Rome]
5 IBENS - Institut de biologie de l'ENS Paris

RapGreen is a modular software package targeted at scientists handling large datasets for phylogenetic analysis. Its primary function is the graphical visualization and exploration of large trees. In addition, RapGreen offers a tree pattern search function to seek evolutionary scenarios among large collections of phylogenetic trees. Other functionalities include tree reconciliation with a given species tree: the detection of duplication or loss events during evolution and tree rooting. Last but not least, RapGreen features the ability to integrate heterogeneous data while visualizing and otherwise analyzing phylogenetic trees.

Domaines: Bio-informatique [q-bio.QM]

Jean-François Dufayard, Stéphanie Bocs, Valentin Guignon, Delphine Larivière, Alexandra Louis, et al.. RapGreen, an interactive software and web package to explore and analyze phylogenetic trees. NAR Genomics and Bioinformatics, 2021, 3 (3), 6 p. ⟨10.1093/nargab/lqab088⟩. ⟨hal-03541670⟩