arXiv subjects

Gabriel Cardona

Publications and source records attributed to Gabriel Cardona.

25 records · Page 2Linked to original sources

arXiv2007

A Perl Package and an Alignment Tool for Phylogenetic Networks

Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of evolutionary events acting at the population level, like recombination between genes, hybridization between lineages, and lateral gene transfer. While most phylogenetics tools implement a wide range of algorithms on phylogenetic trees, there exist only a few applications to work with phylogenetic networks, and there are no open-source libraries either. In order to improve this situation, we have developed a Perl package that relies on the BioPerl bundle and implements many algorithms on phylogenetic networks. We have also developed a Java applet that makes use of the aforementioned Perl package and allows the user to make simple experiments with phylogenetic networks without having to develop a program or Perl script by herself. The Perl package has been accepted as part of the BioPerl bundle. It can be downloaded from http://dmi.uib.es/~gcardona/BioInfo/Bio-PhyloNetwork.tgz. The web-based application is available at http://dmi.uib.es/~gcardona/BioInfo/. The Perl package includes full documentation of all its features.

q-bio.PE↗

arXiv2007

Comparison of Tree-Child Phylogenetic Networks

Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of non-treelike evolutionary events, like recombination, hybridization, or lateral gene transfer. In this paper, we present and study a new class of phylogenetic networks, called tree-child phylogenetic networks, where every non-extant species has some descendant through mutation. We provide an injective representation of these networks as multisets of vectors of natural numbers, their path multiplicity vectors, and we use this representation to define a distance on this class and to give an alignment method for pairs of these networks. To the best of our knowledge, they are respectively the first true distance and the first alignment method defined on a meaningful class of phylogenetic networks strictly extending the class of phylogenetic trees. Simple, polynomial algorithms for reconstructing a tree-child phylogenetic network from its path multiplicity vectors, for computing the distance between two tree-child phylogenetic networks, and for aligning a pair of tree-child phylogenetic networks, are provided, and they have been implemented as a Perl package and a Java applet, and they are available at http://bioinfo.uib.es/~recerca/phylonetworks/mudistance

q-bio.PE↗

arXiv2007

Tripartitions do not always discriminate phylogenetic networks

Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of non-treelike evolutionary events, like recombination, hybridization, or lateral gene transfer. In a recent series of papers devoted to the study of reconstructibility of phylogenetic networks, Moret, Nakhleh, Warnow and collaborators introduced the so-called {tripartition metric for phylogenetic networks. In this paper we show that, in fact, this tripartition metric does not satisfy the separation axiom of distances (zero distance means isomorphism, or, in a more relaxed version, zero distance means indistinguishability in some specific sense) in any of the subclasses of phylogenetic networks where it is claimed to do so. We also present a subclass of phylogenetic networks whose members can be singled out by means of their sets of tripartitions (or even clusters), and hence where the latter can be used to define a meaningful metric.

q-bio.PE↗

arXiv2007

Zeta function and cryptographic exponent of supersingular curves of genus 2

We compute in a direct (not algorithmic) way the zeta function of all supersingular curves of genus 2 over a finite field k, with many geometric automorphisms. We display these computations in an appendix where we select a family of representatives of all these curves up to geometric isomorphism and we exhibit equations and the zeta function of all their twists. As an application we obtain a direct computation of the cryptographic exponent of the Jacobians of these curves.

math.NT↗

arXiv2002

Curves of genus two over fields of even characteristic

In this paper we classify curves of genus two over a perfect field k of characteristic two. We find rational models of curves with a given arithmetic structure for the ramification divisor and we give necessary and sufficient conditions for two models of the same type to be k-isomorphic. As a consequence, we obtain an explicit formula for the number of k-isomorphism classes of curves of genus two over a finite field. Moreover, we prove that the field of moduli of any curve coincides with its field of definition, by exhibiting rational models of curves with any prescribed value of their Igusa invariants. Finally, we use cohomological methods to find, for each rational model, an explicit description of its twists. In this way, we obtain a parameterization of all k-isomorphism classes of curves of genus two in terms of geometric and arithmetic invariants.

math.NT↗

arXiv2002

Field of moduli and field of definition for curves of genus 2

Let M_2 be the moduli space that classifies genus 2 curves. If a curve C is defined over a field k, the corresponding moduli point P=[C] is defined over k. Mestre solved the converse problem for curves with Aut(C) isomorphic to C_2. Given a moduli point defined over k, Mestre finds an obstruction to the existence of a corresponding curve defined over k, that is an element in Br_2(k) not always trivial. In this paper we prove that for all the other possibilities of Aut(C), every moduli point defined over k is represented by a curve defined over k. We also give an explicit construction of such a curve in terms of the coordinates of the moduli point.

math.NT↗

arXiv2002

Curves of genus 2 with group of automorphisms isomorphic to D_8 or D_12

In this paper we classify curves of genus 2 with group of automorphisms isomorphic to D_8 or D_12 over an arbitrary field k (of characteristic different from 2 in the D_8 case and from 2 and 3 in the D_{12} case) up to k-isomorphism. As an application of the classification of curves of genus 2 obtained, we get precise arithmetic information on their elliptic quotients and on their jacobians. Over the field k=Q, we show that the elliptic quotients of the curves with automorphisms D_8 and D_{12} are precisely the Q-curves of degrees 2 and 3, respectively, and we determine which curves have jacobians of GL_2-type.

math.NT↗