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

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Abstract

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.

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Most cited references 11

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Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks.

Daniel Huson, Celine Scornavacca (2012)

Dendroscope 3 is a new program for working with rooted phylogenetic trees and networks. It provides a number of methods for drawing and comparing rooted phylogenetic networks, and for computing them from rooted trees. The program can be used interactively or in command-line mode. The program is written in Java, use of the software is free, and installers for all 3 major operating systems can be downloaded from www.dendroscope.org. [Phylogenetic trees; phylogenetic networks; software.].

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PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics

Michiel Van Bel, Tim Diels, Emmelien Vancaester … (2017)

Abstract PLAZA (https://bioinformatics.psb.ugent.be/plaza) is a plant-oriented online resource for comparative, evolutionary and functional genomics. The PLAZA platform consists of multiple independent instances focusing on different plant clades, while also providing access to a consistent set of reference species. Each PLAZA instance contains structural and functional gene annotations, gene family data and phylogenetic trees and detailed gene colinearity information. A user-friendly web interface makes the necessary tools and visualizations accessible, specific for each data type. Here we present PLAZA 4.0, the latest iteration of the PLAZA framework. This version consists of two new instances (Dicots 4.0 and Monocots 4.0) providing a large increase in newly available species, and offers access to updated and newly implemented tools and visualizations, helping users with the ever-increasing demands for complex and in-depth analyzes. The total number of species across both instances nearly doubles from 37 species in PLAZA 3.0 to 71 species in PLAZA 4.0, with a much broader coverage of crop species (e.g. wheat, palm oil) and species of evolutionary interest (e.g. spruce, Marchantia). The new PLAZA instances can also be accessed by a programming interface through a RESTful web service, thus allowing bioinformaticians to optimally leverage the power of the PLAZA platform.

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Databases of homologous gene families for comparative genomics

Simon Penel, Anne-Muriel Arigon-Chifolleau, Jean-François Dufayard … (2009)

Background Comparative genomics is a central step in many sequence analysis studies, from gene annotation and the identification of new functional regions in genomes, to the study of evolutionary processes at the molecular level (speciation, single gene or whole genome duplications, etc.) and phylogenetics. In that context, databases providing users high quality homologous families and sequence alignments as well as phylogenetic trees based on state of the art algorithms are becoming indispensable. Methods We developed an automated procedure allowing massive all-against-all similarity searches, gene clustering, multiple alignments computation, and phylogenetic trees construction and reconciliation. The application of this procedure to a very large set of sequences is possible through parallel computing on a large computer cluster. Results Three databases were developed using this procedure: HOVERGEN, HOGENOM and HOMOLENS. These databases share the same architecture but differ in their content. HOVERGEN contains sequences from vertebrates, HOGENOM is mainly devoted to completely sequenced microbial organisms, and HOMOLENS is devoted to metazoan genomes from Ensembl. Access to the databases is provided through Web query forms, a general retrieval system and a client-server graphical interface. The later can be used to perform tree-pattern based searches allowing, among other uses, to retrieve sets of orthologous genes. The three databases, as well as the software required to build and query them, can be used or downloaded from the PBIL (Pôle Bioinformatique Lyonnais) site at .

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Author and article information

Contributors

Jean-François Dufayard:

ORCID: https://orcid.org/0000-0002-7427-6822

Stéphanie Bocs

Valentin Guignon:

ORCID: https://orcid.org/0000-0003-0903-6811

Delphine Larivière

Alexandra Louis:

ORCID: https://orcid.org/0000-0001-7032-5650

Nicolas Oubda

Mathieu Rouard:

ORCID: https://orcid.org/0000-0003-0284-1885

Manuel Ruiz

Frédéric de Lamotte

Journal

Journal ID (nlm-ta): NAR Genom Bioinform

Journal ID (iso-abbrev): NAR Genom Bioinform

Journal ID (publisher-id): nargab

Title: NAR Genomics and Bioinformatics

Publisher: Oxford University Press

ISSN (Electronic): 2631-9268

Publication date Collection: September 2021

Publication date (Electronic): 23 September 2021

Publication date PMC-release: 23 September 2021

Volume: 3

Issue: 3

Electronic Location Identifier: lqab088

Affiliations

CIRAD, UMR AGAP Institut , Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France