Exploració per autor "Fernández Sánchez, Jesús"
Ara es mostren els items 11-29 de 29
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Invariant versus classical quartet inference when evolution is heterogeneous across sites and lineages
Fernández Sánchez, Jesús; Casanellas Rius, Marta (2016)
Article
Accés obertOne 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 ... -
Invariants, una aproximació a la filogenètica des de l'àlgebra
Fernández Sánchez, Jesús (2010)
Article
Accés obertEn 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 ... -
Lie Markov model
Sumner, Jeremy; Fernández Sánchez, Jesús; Jarvis, Peter (2012)
Article
Accés obertRecent 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
Accés restringit per política de l'editorialRecent 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. (2015-03-01)
Article
Accés obertContinuous-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. (2013-06)
Report de recerca
Accés obertContinuous-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)
Report de recerca
Accés obertMotivated 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
Accés obertPhylogenetic 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
Accés obertMotivated 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 MATEMÀTICS EN BIOLOGIA | FINAL
Casanellas Rius, Marta; Fernández Sánchez, Jesús; Huguet Casades, Gemma; Ponce Álvarez, Adrián Fernando (Universitat Politècnica de Catalunya, 2023-12-19)
Examen
Accés restringit a la comunitat UPC -
Phylogenetic reconstruction using algebraic geometry
Casanellas Rius, Marta; Fernández Sánchez, Jesús (2010-12-31)
Article
Accés restringit per política de l'editorialA 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 ... -
Rank conditions on phylogenetic networks
Casanellas Rius, Marta; Fernández Sánchez, Jesús (Birkhäuser, 2021)
Capítol de llibre
Accés restringit per política de l'editorialLess rigid than phylogenetic trees, phylogenetic networks allow the description of a wider range of evolutionary events. In this note, we explain how to extend the rank invariants from phylogenetic trees to phylogenetic ... -
Reconstrucción filogenética usando Geometría Algebraica
Casanellas Rius, Marta; Fernández Sánchez, Jesús (2010)
Article
Accés obertUna 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)
Report de recerca
Accés obertRecently 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 ... -
SAQ: semi-algebraic quartet reconstruction
Casanellas Rius, Marta; Fernández Sánchez, Jesús; Garrote López, Marina (2021-01-01)
Article
Accés obertWe present the phylogenetic quartet reconstruction method SAQ (Semi-Algebraic Quartet reconstruction). SAQ is consistent with the most general Markov model of nucleotide substitution and, in particular, it allows for rate ... -
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)
Report de recerca
Accés restringit per acord de confidencialitatWe 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 embedding problem for Markov matrices
Casanellas Rius, Marta; Fernández Sánchez, Jesús; Roca Lacostena, Jordi (2023-01-01)
Article
Accés obertCharacterizing whether a Markov process of discrete random variables has a homogeneous continuous-time realization is a hard problem. In practice, this problem reduces to deciding when a given Markov matrix can be written ... -
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
Accés obert© 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
Accés obertThe 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 ...