1,078 research outputs found
Seqotron: A user-friendly sequence editor for Mac OS X
No full text© 2016 Fourment and Holmes. Background: Accurate multiple sequence alignment is central to bioinformatics and molecular evolutionary analyses. Although sophisticated sequence alignment programs are available, manual adjustments are often required to improve alignment quality. Unfortunately, few programs offer a simple and intuitive way to edit sequence alignments. Results: We present Seqotron, a sequence editor that reads and writes files in a wide variety of sequence formats. Sequences can be easily aligned and manually edited using the mouse and keyboard. The program also allows the user to estimate both phylogenetic trees and distance matrices. Conclusions: Seqotron will benefit researchers who need to manipulate and align complex sequence data. Seqotron is a Mac OS X compatible open source project and is available from Github https://github.com/4ment/seqotron/
Novel non-parametric models to estimate evolutionary rates and divergence times from heterochronous sequence data
No full textBackground: Early methods for estimating divergence times from gene sequence data relied on the assumption of a molecular clock. More sophisticated methods were created to model rate variation and used auto-correlation of rates, local clocks, or the so called "uncorrelated relaxed clock" where substitution rates are assumed to be drawn from a parametric distribution. In the case of Bayesian inference methods the impact of the prior on branching times is not clearly understood, and if the amount of data is limited the posterior could be strongly influenced by the prior. Results: We develop a maximum likelihood method - Physher - that uses local or discrete clocks to estimate evolutionary rates and divergence times from heterochronous sequence data. Using two empirical data sets we show that our discrete clock estimates are similar to those obtained by other methods, and that Physher outperformed some methods in the estimation of the root age of an influenza virus data set. A simulation analysis suggests that Physher can outperform a Bayesian method when the real topology contains two long branches below the root node, even when evolution is strongly clock-like. Conclusions: These results suggest it is advisable to use a variety of methods to estimate evolutionary rates and divergence times from heterochronous sequence data. Physher and the associated data sets used here are available online at. © 2014 Fourment and Holmes; licensee BioMed Central Ltd
Analysis of Mathieu Equation Stable Solutions in the First Zone of Stability
No full textAbstractThe paper presents the results of a homogeneous Mathieu equation studies. Mathieu equation solutions are oscillations, modulated in amplitude and frequency. In the computational experiments we found dependences of the given oscillations on the ratio of the coefficients. These dependences are shown in graphs that can be used for an approximate estimation of the Mathieu equation solutions without integration
Pensar las escalas para pensar las luchas: Autor: Mathieu UHEL
No full textA través de un título sugerente, “pensar las escalas para pensar las luchas”, Mathieu Uhel entreteje la construcción teórico-crítica del concepto escala, generada por la geografía radical anglosajona de finales del siglo XX, con la necesidad/utilidad práctica de la escala para concienciar las luchas sociales. El artículo cumple un doble propósito: por un lado, delinear los elementos de lectura sobre el concepto escala; y, con ello, promover la atención de esta problemática en las luchas contemporáneas. En un primer apartado, Uhel ubica las discusiones académicas en torno a la escala, como herramienta metodológica útil para comprender la complejidad de las sociedades capitalistas; en el segundo apartado, el autor avanza la exposición en torno al contexto de la dimensión escalar del imperialismo capitalista; finalmente, el autor se centra en el rol de la actividad política a escala nacional en la tensa relación entre las imposiciones del capital y la lucha social.Por meio de um título sugestivo, “pensando escalas para pensar lutas”, Mathieu Uhel entrelaça a construção teórico-crítica do conceito de escala, gerado pela geografia radical anglo-saxônica do final do século XX, com a necessidade / utilidade prática escala para aumentar a consciência das lutas sociais. O artigo tem um duplo propósito: por um lado, delinear os elementos de leitura sobre o conceito de escala; e, com isso, promover atenção a esse problema nas lutas contemporâneas. Na primeira seção, Uhel localiza as discussões acadêmicas em torno da escala, como uma ferramenta metodológica útil para compreender a complexidade das sociedades capitalistas; na segunda seção, o autor avança a exposição em torno do contexto da dimensão escalar do imperialismo capitalista; por fim, o autor enfoca o papel da atividade política em escala nacional na tensa relação entre as imposições do capital e a luta social.Mathieu Uhel\u27s suggestive title, “Thinking about scales to think about struggles”, he interweaves the theoretical-critical construction of concept scale, generated by radical Anglo-Saxon geography in the late 20th century, with it´s practical utility to social struggles. The article serves two purposes: on the one hand, Uhel locates academic discussion around scale; and, with this, he promotes attention to this problem in contemporary struggles. In the first section, Uhel locates academic discussions around scale, as a useful methodological tool to understand the complexity of capitalist societies; in the second section, the author advances the argument around the context of the scalar dimension of capitalist imperialism; finally, the author focuses on the role of political activity on a national scale in the tense relationship between the impositions of capital and the social movement
Mathieu Ichou, Les Enfants d’immigrés à l’école
No full textIt is common to hear in the fields of educational and immigration sociology that on average, the children of immigrants do not perform as well in school as children of native-born parents. Mathieu Ichou offers an innovative sociological analysis on a topic that is heavily exploited by political and media discourse, and subject to much scientific controversy. The author takes distance from the homogenized vision of a “second generation” of students who have totally failed academically, and rep..
L'impatto dell'attività tintoria sull'ambiente. Firenze alla fine del Medioevo
No full textThe author aims to examine and categorize the range of dyeings materials used in the Florentine wool and silk textile industries in the late Middle Ages, focusing mainly on those produced within the regional space in order to evaluate the impact of the Florentine dyeing activity on the natural environment and the productive landscape of the Tuscan countryside. In particular, the author establishes a line of demarcation between cultivated and uncultivated resources in order to verify which constitutes an indication of the level of industrial development of medieval textile production. This further focuses on how the transition from the exploitation of wild resources to the exploitation of cultivated resources could reflect a greater degree of economic integration between the countryside and the city and contribute to the formation of a regional economic space
Mathieu de Fossey: su visión del mundo indígena mexicano
No full textThroughout these pages the author shows how Mathieu de Fossey perceived that it was not easy to make indigenous communities fit within the mould of the nation-state which, being based on the liberal and egualitarian ideology, was against the recognition of special regimes, such as those that created a peculiar status for the native population of the American territory during the period of Spanish colonial domination
Mathieu de Fossey: su visión del mundo indígena mexicano
No full textÀ travers ces pages, l’auteur montre comment Mathieu de Fossey avait perçu la difficulté d’insérer le monde des communautés indigènes dans le moule d’un État national qui, accroché à une idéologie libérale égalitaire, refusait d’établir des régimes spéciaux comparables à ceux qui, durant la domination espagnole, avaient reconnu un statut particulier aux populations natives du continent américain.A través de estas páginas se muestra cómo Mathieu de Fossey percibió el difícil acoplamiento del mundo de las comunidades indígenas en el molde de un Estado nacional que, por estar sustentado en la ideología liberal igualitaria, era contrario al reconocimiento de regímenes especiales como los que, durante la dominación española, habían establecido un status peculiar para los aborígenes del territorio americano.Throughout these pages the author shows how Mathieu de Fossey perceived that it was not easy to make indigenous communities fit within the mould of the nation-state which, being based on the liberal and egualitarian ideology, was against the recognition of special regimes, such as those that created a peculiar status for the native population of the American territory during the period of Spanish colonial domination
Investigation of documents persistency on the Web
No full text@inproceedings{CI-Lancieri-2004-2, author = {Lancieri, Luigi and Lecouvey, Mathieu and Glasse, Veronique}, title = {Investigation of documents persistency on the Web}, booktitle = {International conference E-Society 2004 (ES2004), IADIS}, year = {2004}, address = {Spain} }International audienc
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