Capybara: Equivalence ClAss enumeration of coPhylogenY event-BAsed ReconciliAtions

Autor: Yishu Wang, Blerina Sinaimeri, Marie-France Sagot, Arnaud Mary
Přispěvatelé: Baobab, Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Equipe de recherche européenne en algorithmique et biologie formelle et expérimentale (ERABLE), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)
Jazyk: angličtina
Rok vydání: 2020
Předmět:
0106 biological sciences
Statistics and Probability
Source code
Theoretical computer science
Computer science
Process (engineering)
media_common.quotation_subject
Event based
[INFO.INFO-DS]Computer Science [cs]/Data Structures and Algorithms [cs.DS]
Listing (computer)
Rodentia
[SDV.BID]Life Sciences [q-bio]/Biodiversity
010603 evolutionary biology
01 natural sciences
Biochemistry
Equivalence class (music)
03 medical and health sciences
Enumeration
Animals
Molecular Biology
Phylogeny
030304 developmental biology
media_common
0303 health sciences
Phylogenetic tree
[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
Computer Science Applications
Computational Mathematics
Computational Theory and Mathematics
[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]
Algorithms
Software
Zdroj: Bioinformatics
Bioinformatics, Oxford University Press (OUP), 2020, 36 (14), pp.4197-4199. ⟨10.1093/bioinformatics/btaa498⟩
Bioinformatics, 2020, 36 (14), pp.4197-4199. ⟨10.1093/bioinformatics/btaa498⟩
ISSN: 1367-4803
1367-4811
DOI: 10.1093/bioinformatics/btaa498⟩
Popis: Motivation Phylogenetic tree reconciliation is the method of choice in analyzing host-symbiont systems. Despite the many reconciliation tools that have been proposed in the literature, two main issues remain unresolved: (i) listing suboptimal solutions (i.e. whose score is ‘close’ to the optimal ones) and (ii) listing only solutions that are biologically different ‘enough’. The first issue arises because the optimal solutions are not always the ones biologically most significant; providing many suboptimal solutions as alternatives for the optimal ones is thus very useful. The second one is related to the difficulty to analyze an often huge number of optimal solutions. In this article, we propose Capybara that addresses both of these problems in an efficient way. Furthermore, it includes a tool for visualizing the solutions that significantly helps the user in the process of analyzing the results. Availability and implementation The source code, documentation and binaries for all platforms are freely available at https://capybara-doc.readthedocs.io/. Contact yishu.wang@univ-lyon1.fr or blerina.sinaimeri@inria.fr Supplementary information Supplementary data are available at Bioinformatics online.
Databáze: OpenAIRE
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