Now showing items 1-19 of 19

  • A new phylogenetic reconstruction method based on invariants 

    Casanellas Rius, Marta; Fernández Sánchez, Jesús (2005)
    Article
    Open Access
    An attempt to use phylogenetic invariants for tree reconstruction was made at the end of the 80s and the beginning of the 90s by several authors (the initial idea due to Lake [Lake, 1987] and Cavender and Felsenstein [Cavender ...
  • EXPRESSIO GRAFICA I DISENY ASSISTIT PER ORDINADOR (Examen 1r Quadr.) 

    Fernández Sánchez, Jesús (Universitat Politècnica de Catalunya, 2004-01-14)
    Exam
    Restricted access to the UPC academic community
  • EXPRESSIO GRAFICA I DISENY ASSISTIT PER ORDINADOR (Examen 2n Quadr.) 

    Fernández Sánchez, Jesús (Universitat Politècnica de Catalunya, 2003-04-03)
    Exam
    Restricted access to the UPC academic community
  • EXPRESSIO GRAFICA I DISENY ASSISTIT PER ORDINADOR (Examen 2n Quadr.) 

    Fernández Sánchez, Jesús (Universitat Politècnica de Catalunya, 2002-06-17)
    Exam
    Restricted access to the UPC academic community
  • Invariants, una aproximació a la filogenètica des de l'àlgebra 

    Fernández Sánchez, Jesús (2010)
    Article
    Open Access
    En els darrers anys, una nova aproximació a la reconstrucció filogenètica basada en tècniques provinents de l’àlgebra s’ha estat consolidant. Fixat un model evolutiu per a un conjunt donat d’espècies, els invariants són ...
  • 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 ...
  • Lie Markov model 

    Sumner, Jeremy; Fernández Sánchez, Jesús; Jarvis, Peter (2012)
    Article
    Open Access
    Recent work has discussed the importance of multiplicative closure for the Markov mod- els used in phylogenetics. For continuous-time Markov chains, a sufficient condition for multiplicative closure of a model class is ...
  • Lie Markov models 

    Sumner, Jeremy; Fernández Sánchez, Jesús; Jarvis, Peter (2012-04-07)
    Article
    Restricted access - publisher's policy
    Recent work has discussed the importance of multiplicative closure for the Markov models used in phylogenetics. For continuous-time Markov chains, a sufficient condition for multiplicative closure of a model class is ensured ...
  • Lie Markov models with purine/pyrimidine symmetry 

    Fernández Sánchez, Jesús; Sumner, Jeremy; Jarvis, Peter; Woodhams, Michael D. (2013-06)
    External research report
    Open Access
    Continuous-time Markov chains are a standard tool in phylogenetic inference. If homogeneity is assumed, the chain is formulated by specifying time-independent rates of substitutions between states in the chain. In applications, ...
  • Lie Markov models with purine/pyrimidine symmetry 

    Fernández Sánchez, Jesús; Sumner, Jeremy; Jarvis, Peter; Woodhams, Michael D. (2015-03-01)
    Article
    Open Access
    Continuous-time Markov chains are a standard tool in phylogenetic inference. If homogeneity is assumed, the chain is formulated by specifying time-independent rates of substitutions between states in the chain. In applications, ...
  • 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
    Restricted access - publisher's policy
    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 ...
  • 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 ...
  • Testing of the three multiplicatively closed (Lie Markov) model heirarchies which respect purine/pyrimidine, Watson-Crick, and amino/keto nucleotide groupings 

    Woodhams, Michael D.; Fernández Sánchez, Jesús; Sumner, Jeremy (2014-03)
    External research report
    Restricted access - confidentiality agreement
    We present three hierarchies of Lie Markov models of DNA sequence evolution. These models are (locally) “multiplicatively closed,” meaning that the composition of two Markov matrices in the model results, with some (rare) ...
  • 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 ...