O Gascuel

..Gene expression data have been widely used in the recent years to help functional annotation in an intra-species way via the so-called Guilt By Association (GBA) principle...

..falciparum gene models and 3) pinpointing genes displaying protein polymorphism between the FcB1 and 3D7 strains...

..We propose an influenza-specific amino acid substitution model to enhance the understanding of the evolution of influenza viruses...

..Non-homology methods are thus needed to obtain functional clues for these uncharacterized genes...

..But available agglomerative algorithms cannot deal with incomplete matrices...

..0 substitutions per site), the error reduction may even rise above 50%, while the probability of finding the correct tree may be augmented by as much as 15%...

..i.d. models may no longer be valid. In this paper, we assemble a collection of results to analyse various approaches for inferring ancestral information with increasing accuracy as the number of taxa increases...

..The origins of this story lie in a paper by Pauplin (2000) though its continuation has unfolded in more mathematically inclined literature. Our aim here is to make these findings more widely accessible...

..Simulations show that BIONJ significantly outperforms NJ...

..Our data, models, and software are available for download from http://atgc.lirmm.fr/phyml-structure/...

..We apply this approach to tandemly repeated human Zinc finger genes and observe that a much better duplication tree is obtained by our method than using any other program...

..This new method is implemented in the PHYML program, which is freely available on our web page: http://www.lirmm.fr/w3ifa/MAAS/...

..Results with the test alignments from Pfam are analogous. LG and a PHYML implementation can be downloaded from http://atgc.lirmm.fr/LG...

..The results clearly show that DTSCORE is more accurate than all the other methods we studied. Finally, we report the results of DTSCORE on a real dataset. Supplementary information: http://www.lirmm.fr/w3ifa/MAAS/..

..Finally, a data set of Maoricicada species sequences is analyzed, which confirms the advantage of our method...

..When this occurs, the resulting trees may still show some of the defects (e.g. long branch attraction) of starting trees obtained using fast distance or parsimony programs...

..This difference may explain the gap in reconstruction accuracy observed in practice between OLS + ME and BME (which forms the basis of popular programs such as NJ and FastME)...

..In this work, we propose an approach to evaluate the stability of clusters derived from hierarchical clustering by taking repeated measurements into account...

..However, numerous domains may be missed in highly divergent proteins. This is the case for Plasmodium falciparum proteins, the main causal agent of human malaria...

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..All our models and a PhyML implementation are available from http://atgc.lirmm.fr/mixtures...

..We apply it, learning on the HSSP database, and observe that a set of 20 profiles is enough to provide a better statistical fit than currently available empirical matrices (WAG, JTT), in particular on saturated data...

..5% for BioNJ and Weighbor, respectively). Moreover, this combination requires only about 1.5 min to infer a phylogeny of 96 sequences composed of 1,200 nucleotides, as compared with 6.5 h for FastDNAml on the same machine (PC 466 MHz)...

..2002, Syst. Biol. 51: 652-664) that involves 48 genes of 75 placental mammals. The results indicate that these genes have strong rate heterogeneity and confirm the simulation conclusions...

..We illustrate the strengths and pitfalls of this program through the analysis of a real data set. PhyML v3.0 is available from (http://atgc_montpellier.fr/phyml/)...

..Overall, our tests show that the last version (3.0) of PhyML is fast, accurate, stable, and ready to use. A Web server and binary files are available from http://www.atgc-montpellier.fr/phyml/...

..The recurrence relation also suggests efficient algorithms to recognize duplication trees and to generate random duplication trees for simulation. We present a linear-time recognition algorithm...

..Interestingly, the covarion parameter has little effect on the tree quality for any of the algorithms. FASTME is freely available on the web...

..These results demonstrate the usefulness and accuracy of our (simple) approach, which should apply to other function or interaction prediction problems...

..Peptide hormones and their receptors are important diagnostic and therapeutic targets, and our results suggest that spexin and augurin are novel peptide hormones likely to be involved in physiological homeostasis...

..Moreover, this BME scheme yields a very significant improvement over NJ and other distance-based algorithms, especially with large trees, in terms of topological accuracy...

..We show, on simulated data, that those algorithms can be used to improve phylogenetic inference of tandemly repeated gene families. An application on a published phylogeny of KRAB zinc finger genes is presented...

..It also describes how to estimate evolutionary distances from DNA and proteins, how to perform bootstrap analysis, and how to use CLUSTAL to compute both a sequence alignment and a phylogenetic tree...

..The server and its documentation are available at http://atgc.lirmm.fr/phyml...

..scmbb.ulb.ac.be/rsat/). CONTACT: SUPPLEMENTARY INFORMATION: The complete datasets and results are available at http://rsat.scmbb.ulb.ac.be/rsat/data/published_data/Gonze_MET_PHO/..

..The aLRT is implemented within the algorithm used by the recent fast maximum likelihood tree estimation program PHYML (Guindon and Gascuel, 2003)...

..Crown placental mammalian diversification appears to be largely the result of ancient plate tectonic events that allowed time for convergent phenotypes to evolve in the descendant clades...