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4 de septiembre de 2017

Course on Metagenomics and Barcoding in Crete, March 19-23, 2018

Transmitting Science is offering a new course on its new venue: AN INTRODUCTION TO METAGENOMICS AND METABARCODING.

Dates: March 19-23, 2018.

Place: Heraklion (Crete, Greece).

Instructor: Dr. M. Lisandra Zepeda-Mendoza (Chr. Hansen – Bacterial Physiology & Improvement, Denmark).

Metagenomics is the study of the collection of genomes in an environment. Environments as diverse as Antarctic lakes, hot springs, or the human gut can be biologically characterized by extracting and sequencing DNA from samples taken from them. A characteristic of many of these samples is their complexity, posing difficulties to their analysis and characterization. However, metagenomics allows the taxonomic and functional characterization of samples. These two kinds of characterizations also enable the comparison of different habitats for biodiversity assessment.
In this course students will be introduced to the command line environment used to analyze high-throughput sequencing data (HTS). The initial cleaning steps that must be performed on every HTS dataset will be described and we will use the processed data for proper functional and taxonomical characterization of a metagenomic dataset. We will use methods such as mapping to whole genome databases, de novo assembly, gene annotation, building of non-redundant gene catalogue, and metagenomic species concept identification. Due to the wide usage of metabarcoding for the taxonomic characterization of an environment, we will also discuss amplicon sequencing strategies and data analysis. The course will be based on both theory and hands-on exercises.

5 de junio de 2017

El artículo en Cladistics que no leerán los que hacen verosimilitud y probs Bayesianas

"Is there any reason, other than esprit de corps, to explain why, in many journals, it became almost impossible to publish a paper using parsimony as the only method?"

Pablo A. Goloboff, Ambrosio Torres and J. Salvador Arias. 2017. Weighted parsimony outperforms other methods of phylogenetic inference under models appropriate for morphology. Cladistics

Aqui esta el resumen.

Abstract One of the lasting controversies in phylogenetic inference is the degree to which specific evolutionary models should influence the choice of methods. Model-based approaches to phylogenetic inference (likelihood, Bayesian) are defended on the premise that without explicit statistical models there is no science, and parsimony is defended on the grounds that it provides the best rationalization of the data, while refraining from assigning specific probabilities to trees or character-state reconstructions. Authors who favour model-based approaches often focus on the statistical properties of the methods and models themselves, but this is of only limited use in deciding the best method for phylogenetic inference—such decision also requires considering the conditions of evolution that prevail in nature. Another approach is to compare the performance of parsimony and model- based methods in simulations, which traditionally have been used to defend the use of models of evolution for DNA sequences. Some recent papers, however, have promoted the use of model-based approaches to phylogenetic inference for discrete morpho- logical data as well. These papers simulated data under models already known to be unfavourable to parsimony, and modelled morphological evolution as if it evolved just like DNA, with probabilities of change for all characters changing in concert along tree branches. The present paper discusses these issues, showing that under reasonable and less restrictive models of evolution for discrete characters, equally weighted parsimony performs as well or better than model-based methods, and that parsimony under implied weights clearly outperforms all other methods. © The Willi Hennig Society 2017.

12 de abril de 2017

Que buen sentido de humor tenemos los taxónomos

Neopalpa donaldtrumpi, named for the distinctive wave of yellowish-white scales that cascades forward from the moth’s head.
Un entomólogo canadiense recién nombró una nueva especie con dedicatoria especial a Donald Trump.
El artículo fue publicado en  ZooKeys y Vazrick Nazariel, el autor,  explica "The specific epithet is selected because of the resemblance of the scales on the frons (head) of the moth to Mr. Trump’s hairstyle."
Información general esta aqui:
Pero hay más ... no solo es por la melena al frente .....

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