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      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.

          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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            Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases.

            Comparative sequence analysis is widely used to study genome function and evolution. This approach first requires the identification of homologous genes and then the interpretation of their homology relationships (orthology or paralogy). To provide help in this complex task, we developed three databases of homologous genes containing sequences, multiple alignments and phylogenetic trees: HOBACGEN, HOVERGEN and HOGENOM. In this paper, we present two new tools for automating the search for orthologs or paralogs in these databases. First, we have developed and implemented an algorithm to infer speciation and duplication events by comparison of gene and species trees (tree reconciliation). Second, we have developed a general method to search in our databases the gene families for which the tree topology matches a peculiar tree pattern. This algorithm of unordered tree pattern matching has been implemented in the FamFetch graphical interface. With the help of a graphical editor, the user can specify the topology of the tree pattern, and set constraints on its nodes and leaves. Then, this pattern is compared with all the phylogenetic trees of the database, to retrieve the families in which one or several occurrences of this pattern are found. By specifying ad hoc patterns, it is therefore possible to identify orthologs in our databases.
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              Databases of homologous gene families for comparative genomics

              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
                Journal
                NAR Genom Bioinform
                NAR Genom Bioinform
                nargab
                NAR Genomics and Bioinformatics
                Oxford University Press
                2631-9268
                September 2021
                23 September 2021
                23 September 2021
                : 3
                : 3
                Affiliations
                CIRAD, UMR AGAP Institut , Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
                French Institute of Bioinformatics (IFB ) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
                CIRAD, UMR AGAP Institut , Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
                French Institute of Bioinformatics (IFB ) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
                French Institute of Bioinformatics (IFB ) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
                Bioversity International , Parc Scientifique Agropolis II, 34397, Montpellier, France
                CIRAD, UMR AGAP Institut , Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
                French Institute of Bioinformatics (IFB ) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
                IBENS, Institut de Biologie de l’ENS , Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
                CIRAD, UMR AGAP Institut , Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
                French Institute of Bioinformatics (IFB ) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
                French Institute of Bioinformatics (IFB ) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
                Bioversity International , Parc Scientifique Agropolis II, 34397, Montpellier, France
                CIRAD, UMR AGAP Institut , Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
                French Institute of Bioinformatics (IFB ) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
                French Institute of Bioinformatics (IFB ) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, F-34398 Montpellier, France
                UMR AGAP Institut, Univ Montpellier , CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
                Author notes
                To whom correspondence should be addressed. Tel : +33 4 67 61 65 12; Mob: +33 6 16 78 31 64; Fax : +33 4 67 61 56 05; Email: jean-francois.dufayard@ 123456cirad.fr
                Article
                lqab088
                10.1093/nargab/lqab088
                8459725
                © The Author(s) 2021. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License ( https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@ 123456oup.com

                Page count
                Pages: 6
                Product
                Funding
                Funded by: French National Research Agency, DOI 10.13039/501100001665;
                Award ID: ANR- 08-GENO118
                Award ID: ANR-10- BINF-03–04
                Funded by: Institut National de la Recherche Agronomique, DOI 10.13039/501100006488;
                Categories
                AcademicSubjects/SCI00030
                AcademicSubjects/SCI00980
                AcademicSubjects/SCI01060
                AcademicSubjects/SCI01140
                AcademicSubjects/SCI01180
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