arXiv subjects
Publications and source records attributed to Francesc Rossello.
We prove that Nakhleh's latest dissimilarity measure for phylogenetic networks separates distinguishable phylogenetic networks, and that a slight modification of it provides a true distance on the class of all 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.
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
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.
The relationship between two important problems in tree pattern matching, the largest common subtree and the smallest common supertree problems, is established by means of simple constructions, which allow one to obtain a largest common subtree of two trees from a smallest common supertree of them, and vice versa. These constructions are the same for isomorphic, homeomorphic, topological, and minor embeddings, they take only time linear in the size of the trees, and they turn out to have a clear algebraic meaning.
The search for similarity and dissimilarity measures on phylogenetic trees has been motivated by the computation of consensus trees, the search by similarity in phylogenetic databases, and the assessment of clustering results in bioinformatics. The transposition distance for fully resolved phylogenetic trees is a recent addition to the extensive collection of available metrics for comparing phylogenetic trees. In this paper, we generalize the transposition distance from fully resolved to arbitrary phylogenetic trees, through a construction that involves an embedding of the set of phylogenetic trees with a fixed number of labeled leaves into a symmetric group and a generalization of Reidys-Stadler's involution metric for RNA contact structures. We also present simple linear-time algorithms for computing it.
Compatibility of phylogenetic trees is the most important concept underlying widely-used methods for assessing the agreement of different phylogenetic trees with overlapping taxa and combining them into common supertrees to reveal the tree of life. The notion of ancestral compatibility of phylogenetic trees with nested taxa was introduced by Semple et al in 2004. In this paper we analyze in detail the meaning of this compatibility from the points of view of the local structure of the trees, of the existence of embeddings into a common supertree, and of the joint properties of their cluster representations. Our analysis leads to a very simple polynomial-time algorithm for testing this compatibility, which we have implemented and is freely available for download from the BioPerl collection of Perl modules for computational biology.
In this paper we introduce a fuzzy version of symport/antiport membrane systems. Our fuzzy membrane systems handle possibly inexact copies of reactives and their rules are endowed with threshold functions that determine whether a rule can be applied or not to a given set of objects, depending of the degree of accuracy of these objects to the reactives specified in the rule. We prove that these fuzzy membrane systems generate exactly the recursively enumerable finite-valued fuzzy sets of natural numbers.
In this paper we model several simple biochemical operations on RNA molecules that modify their secondary structure by means of a suitable variation of Große-Rhode's Algebra Transformation Systems.
We compute explicitly several abstract metrics for RNA secondary structures defined by Reidys and Stadler.