The inference of gene trees with species trees

Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species. Although the histories of genes and species are tightly linked, they are seldom identical, because genes duplicate, are lost or horizontally transferred, and because alleles can co-exist in populations for periods that may span several speciation events. Building models describing the relationship between gene and species trees can thus improve the reconstruction of gene trees when a species tree is known, and vice-versa. Several approaches have been proposed to solve the problem in one direction or the other, but in general neither gene trees nor species trees are known. Only a few studies have attempted to jointly infer gene trees and species trees. In this article we review the various models that have been used to describe the relationship between gene trees and species trees. These models account for gene duplication and loss, transfer or incomplete lineage sorting. Some of them consider several types of events together, but none exists currently that considers the full repertoire of processes that generate gene trees along the species tree. Simulations as well as empirical studies on genomic data show that combining gene tree-species tree models with models of sequence evolution improves gene tree reconstruction. In turn, these better gene trees provide a better basis for studying genome evolution or reconstructing ancestral chromosomes and ancestral gene sequences. We predict that gene tree-species tree methods that can deal with genomic data sets will be instrumental to advancing our understanding of genomic evolution.Comment: Review article in relation to the "Mathematical and Computational Evolutionary Biology" conference, Montpellier, 201

Grasp Recognition and Manipulation with the

Summary. We describe a novel user interface for natural, whole hand interaction with 3D environments. Our interface uses a graspable device called the Tango, which looks like a ball but measures contact pressures on its surface at 256 tactual elements (taxels) at a high rate (100 Hz). The acceleration of the device is also measured. The key idea is to use this information to recognize the shape and movement of the user’s hand grasping the object. This allows the user to interact with 3D virtual objects using a hand avatar. The interface provides passive force feedback, and is easier to use than interfaces that require wearing gloves or other sensors on the hand. We describe a rotationally invariant matching algorithm for recognizing the hand shape from examples of previous interaction collected with motion capture. We also describe examples of 3D interaction using our system.

The half-sample method for testing parametric regressive and autoregressive models of order 1

Theme 4 - Simulation et optimisation de systemes complexes. Projet is2SIGLEAvailable from INIST (FR), Document Supply Service, under shelf-number : 14802 E, issue : a.1998 n.3418 / INIST-CNRS - Institut de l'Information Scientifique et TechniqueFRFranc

Generation de codes adjoints : traitement de la trajectoire du modele direct

Theme 4 - Simulation et optimisation de systemes complexes. Projet IdoptAvailable from INIST (FR), Document Supply Service, under shelf-number : 14802 E, issue : a.1998 n.3405 / INIST-CNRS - Institut de l'Information Scientifique et TechniqueSIGLEFRFranc

Advanced modelling and verification techniques applied to a cluster file system

Theme 1 - Reseaux et systemes. Projet VASYSIGLEAvailable from INIST (FR), Document Supply Service, under shelf-number : 14802 E, issue : a.1998 n.3416 / INIST-CNRS - Institut de l'Information Scientifique et TechniqueFRFranc

Choosing models in model-based clustering and discriminant analysis

Theme 4 - Simulation et optimisation de systemes complexes. Projet IS2Available from INIST (FR), Document Supply Service, under shelf-number : 14802 E, issue : a.1998 n.3509 / INIST-CNRS - Institut de l'Information Scientifique et TechniqueSIGLEFRFranc

A quasi-score marginal approach in generalized linear mixed model

Theme 4 - Simulation et optimisation des systemes complexes. Projet IS2SIGLEAvailable from INIST (FR), Document Supply Service, under shelf-number : 14802 E, issue : a.1998 n.3522 / INIST-CNRS - Institut de l'Information Scientifique et TechniqueFRFranc

An automatic correcting method

Theme 2 - Genie logiciel et calcul symbolique - Projet ArenaireAvailable from INIST (FR), Document Supply Service, under shelf-number : 14802 E, issue : a.2001 n.4204 / INIST-CNRS - Institut de l'Information Scientifique et TechniqueSIGLEFRFranc

Efficient diagnostic generation for boolean equation systems

Theme 1 - Reseaux et systemes - Projet VASYSIGLEAvailable from INIST (FR), Document Supply Service, under shelf-number : 14802 E, issue : a.2000 n.3861 / INIST-CNRS - Institut de l'Information Scientifique et TechniqueFRFranc