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The MultiFurcating Neighbor-Joining Algorithm for Reconstructing Polytomic Phylogenetic Trees

  • Dades identificatives

    Identificador: imarina:9331068
    Autors:
    Fernandez, AlbertoSegura-Alabart, NataliaSerratosa, Francesc
    Resum:
    Results from phylogenetic analyses that study the evolution of species according to their biological characteristics are frequently structured as phylogenetic trees. One of the most widely used methods for reconstructing them is the distance-based method known as the neighbor-joining (NJ) algorithm. It is known that the NJ algorithm can produce different phylogenetic trees depending on the order of the taxa in the input matrix of evolutionary distances, because the method only yields bifurcating branches or dichotomies. According to this, results and conclusions published in articles that only calculate one of the possible dichotomic phylogenetic trees are somehow biased. We have generalized the formulas used in the NJ algorithm to cope with Multifurcating branches or polytomies, and we have called this new variant of the method the multifurcating neighbor-joining (MFNJ) algorithm. Instead of the dichotomic phylogenetic trees reconstructed by the NJ algorithm, the MFNJ algorithm produces polytomic phylogenetic trees. The main advantage of using the MFNJ algorithm is that only one phylogenetic tree can be obtained, which makes the experimental section of any study completely reproducible and unbiased to external issues such as the input order of taxa.© 2023. The Author(s).
  • Altres:

    Autor segons l'article: Fernandez, Alberto; Segura-Alabart, Natalia; Serratosa, Francesc
    Departament: Enginyeria Informàtica i Matemàtiques Enginyeria Química
    Autor/s de la URV: Fernández Sabater, Alberto / Segura Alabart, Natàlia / Serratosa Casanelles, Francesc d'Assís
    Paraules clau: Ties in proximity Polytomy Phylogeny Neighbor-joining Models, genetic Distance-based methods Construction Algorithms ties in proximity saitou polytomy neighbor-joining
    Resum: Results from phylogenetic analyses that study the evolution of species according to their biological characteristics are frequently structured as phylogenetic trees. One of the most widely used methods for reconstructing them is the distance-based method known as the neighbor-joining (NJ) algorithm. It is known that the NJ algorithm can produce different phylogenetic trees depending on the order of the taxa in the input matrix of evolutionary distances, because the method only yields bifurcating branches or dichotomies. According to this, results and conclusions published in articles that only calculate one of the possible dichotomic phylogenetic trees are somehow biased. We have generalized the formulas used in the NJ algorithm to cope with Multifurcating branches or polytomies, and we have called this new variant of the method the multifurcating neighbor-joining (MFNJ) algorithm. Instead of the dichotomic phylogenetic trees reconstructed by the NJ algorithm, the MFNJ algorithm produces polytomic phylogenetic trees. The main advantage of using the MFNJ algorithm is that only one phylogenetic tree can be obtained, which makes the experimental section of any study completely reproducible and unbiased to external issues such as the input order of taxa.© 2023. The Author(s).
    Àrees temàtiques: Molecular biology Medicina veterinaria Medicina i Genetics & heredity Genetics General medicine Evolutionary biology Ecology, evolution, behavior and systematics Ciências biológicas iii Ciências biológicas ii Ciências biológicas i Biotecnología Biology, miscellaneous Biodiversidade Biochemistry & molecular biology
    Accès a la llicència d'ús: https://creativecommons.org/licenses/by/3.0/es/
    Adreça de correu electrònic de l'autor: natalia.segura@urv.cat natalia.segura@urv.cat natalia.segura@urv.cat alberto.fernandez@urv.cat francesc.serratosa@urv.cat
    Identificador de l'autor: 0000-0002-1241-1646 0000-0001-6112-5913
    Data d'alta del registre: 2024-10-12
    Versió de l'article dipositat: info:eu-repo/semantics/publishedVersion
    Enllaç font original: https://link.springer.com/article/10.1007/s00239-023-10134-z
    URL Document de llicència: https://repositori.urv.cat/ca/proteccio-de-dades/
    Referència a l'article segons font original: Journal Of Molecular Evolution. 91 (6): 773-779
    Referència de l'ítem segons les normes APA: Fernandez, Alberto; Segura-Alabart, Natalia; Serratosa, Francesc (2023). The MultiFurcating Neighbor-Joining Algorithm for Reconstructing Polytomic Phylogenetic Trees. Journal Of Molecular Evolution, 91(6), 773-779. DOI: 10.1007/s00239-023-10134-z
    DOI de l'article: 10.1007/s00239-023-10134-z
    Entitat: Universitat Rovira i Virgili
    Any de publicació de la revista: 2023
    Tipus de publicació: Journal Publications
  • Paraules clau:

    Biochemistry & Molecular Biology,Biology, Miscellaneous,Ecology, Evolution, Behavior and Systematics,Evolutionary Biology,Genetics,Genetics & Heredity,Molecular Biology
    Ties in proximity
    Polytomy
    Phylogeny
    Neighbor-joining
    Models, genetic
    Distance-based methods
    Construction
    Algorithms
    ties in proximity
    saitou
    polytomy
    neighbor-joining
    Molecular biology
    Medicina veterinaria
    Medicina i
    Genetics & heredity
    Genetics
    General medicine
    Evolutionary biology
    Ecology, evolution, behavior and systematics
    Ciências biológicas iii
    Ciências biológicas ii
    Ciências biológicas i
    Biotecnología
    Biology, miscellaneous
    Biodiversidade
    Biochemistry & molecular biology
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