Now showing items 21-37 of 37

    • EMtree for phylogenetic topology reconstruction on nonhomogeneous data 

      Ibáñez Marcelo, Esther; Casanellas Rius, Marta (2014-06-17)
      Article
      Open Access
    • Genètica i geometria algebraica 

      Casanellas Rius, Marta (2005-03-03)
      Audiovisual
      Open Access
      "... Les varietats algebraiques apareixen de manera natural en considerar models estadístics empleats en genòmica i filogenètica. Explicarem quina és la relació entre aquests models estadístics i la geometria algebraica. ...
    • GenNon-h: Generating multiple sequence alignments on nonhomogeneous phylogenetic trees 

      Kedzierska, A.M.; Casanellas Rius, Marta (2012-08-28)
      Article
      Open Access
      Background: A number of software packages are available to generate DNA multiple sequence alignments (MSAs) evolved under continuous-time Markov processes on phylogenetic trees. On the other hand, methods of simulating the ...
    • Invariant versus classical quartet inference when evolution is heterogeneous across sites and lineages 

      Fernández Sánchez, Jesús; Casanellas Rius, Marta (2016)
      Article
      Open Access
      One reason why classical phylogenetic reconstruction methods fail to correctly infer the underlying topology is because they assume oversimplified models. In this article, we propose a quartet reconstruction method consistent ...
    • Local description of phylogenetic group-based models 

      Casanellas Rius, Marta; Fernández Sánchez, Jesús; Michalek, Mateusz (2013-12)
      External research report
      Open Access
      Motivated by phylogenetics, our aim is to obtain a system of equations that de ne a phylogenetic variety on an open set containing the biologically meaningful points. In this paper we consider phylogenetic varieties de ...
    • Local equations for equivariant evolutionary models 

      Casanellas Rius, Marta; Fernández Sánchez, Jesús; Michalek, Mateusz (2017-07-31)
      Article
      Open Access
      Phylogenetic varieties related to equivariant substitution models have been studied largely in the last years. One of the main objectives has been finding a set of generators of the ideal of these varieties, but this has ...
    • Low degree equations for phylogenetic group-based models 

      Casanellas Rius, Marta; Fernández Sánchez, Jesús; Michalek, Mateusz (2015)
      Article
      Open Access
      Motivated by phylogenetics, our aim is to obtain a system of low degree equations that define a phylogenetic variety on an open set containing the biologically meaningful points. In this paper we consider phylogenetic ...
    • Models algebraics en filogenètica 

      Casanellas Rius, Marta (2005)
      Article
      Open Access
      En aquest article fem una introducci´o a les aplicacions de la geometria algebraica en filogen`etica. Gr`acies a qu`e gran part dels models evolutius usats en filogen`etica corresponen a varietats algebraiques, l’ideal ...
    • Phylogenetic mixtures and linear invariants for equal input models 

      Casanellas Rius, Marta; Steel, Mike (2016-09-07)
      Article
      Open Access
      The reconstruction of phylogenetic trees from molecular sequence data relies on modelling site substitutions by a Markov process, or a mixture of such processes. In general, allowing mixed processes can result in different ...
    • Phylogenetic reconstruction using algebraic geometry 

      Casanellas Rius, Marta; Fernández Sánchez, Jesús (2010-12-31)
      Article
      Restricted access - publisher's policy
      A new approach to phylogenetic reconstruction has been emerging in the last years. Given an evolutionary model, the joint probability distribution of the nucleotides for these species satisfy some algebraic constraints ...
    • Reconstrucción filogenética usando Geometría Algebraica 

      Casanellas Rius, Marta; Fernández Sánchez, Jesús (2010)
      Article
      Open Access
      Una nueva aproximación a la reconstrucción filogenética basada en la geometría algebraica está ganando fuerza en los últimos años. Fijado un modelo evolutivo para un conjunto de especies, las distribuciones teóricas de ...
    • Relevant phylogenetic invariants of evolutionary models 

      Casanellas Rius, Marta; Fernández Sánchez, Jesús (2010-01)
      External research report
      Open Access
      Recently there have been several attempts to provide a whole set of generators of the ideal of the algebraic variety associated to a phylogenetic tree evolving under an algebraic model. These algebraic varieties have been ...
    • SPIn: model selection for phylogenetic mixtures via linear invariants 

      Kedzierska, A.M.; Drton, M.; Guigó, Roderic; Casanellas Rius, Marta (2011-10)
      Article
      Restricted access - publisher's policy
      In phylogenetic inference, an evolutionarymodel describes the substitution processes along each edge of a phylogenetic tree. Misspecification of the model has important implications for the analysis of phylogenetic data. ...
    • Tapas of algebraic statistics 

      Casanellas Rius, Marta (2018-09-01)
      Article
      Open Access
    • The inertia of the symmetric approximation for low-rank matrices 

      Casanellas Rius, Marta; Fernández Sánchez, Jesús; Garrote López, Marina (Taylor & Francis, 2017-11-10)
      Article
      Open Access
      © 2017 Informa UK Limited, trading as Taylor & Francis Group In many areas of applied linear algebra, it is necessary to work with matrix approximations. A usual situation occurs when a matrix obtained from experimental ...
    • The space of phylogenetic mixtures for equivariant models 

      Casanellas Rius, Marta; Fernández Sánchez, Jesús; Kedzierska, A.M. (2012-11-28)
      Article
      Open Access
      The selection of the most suitable evolutionary model to analyze the given molecular data is usually left to biologist's choice. In his famous book, J Felsenstein suggested that certain linear equations satisfied by the ...
    • Topologia Algebraica (examen 2n quadrim) 

      Casanellas Rius, Marta (Universitat Politècnica de Catalunya, 2008-03-05)
      Exam
      Restricted access to the UPC academic community