Curso online en directo: Morphological phylogenetics: principles, applications, and techniques, Sept 23-Oct 11, 2024

Ya se ha abierto la inscripción para el curso Morphological phylogenetics: principles, applications, and techniques. 6ª Edición. Este curso se impartirá en directo online (sincrónico). Máximo 18 participantes.

FECHAS Y HORARIO: sesiones en directo el 23, 25, 27, y 30 de septiembre y el 2, 4, 7, 9, y 11 de octubre, 2024; de 16:00 a 19:30 (zona horaria de Madrid).

RESUMEN DEL CURSO (en inglés, que es el idioma en el que se impartirà el mismo)

An accurate reconstruction of evolutionary relationships among species is the cornerstone of evolutionary biology. Building phylogenetic trees thus provides the fundamental framework upon which systematic, biogeographic and evolutionary research operates. Morphological phylogenetics provides a unique toolkit for inferring relationships, considering that the vast majority of the species that have ever lived are now extinct and can only be assessed based on morphological data. 

Additionally, combining fossils and morphological data with molecular data from extant species is becoming the most comprehensive method of assessing phylogenetic relationships on deep time and the time of origin of major evolutionary lineages. In this course, we will focus on the analysis of morphological data (and combining morphological data with molecular data) using multiple optimality criteria for phylogenetic inference. 

We will discuss the best available approaches to construct morphological data sets and their impact on phylogenies. We will follow with theory and hands-on practice of phylogenetic programs using maximum parsimony, maximum likelihood and Bayesian inference. 

Participants will learn how to combine morphological and molecular data for total evidence analyses, how to conduct time-calibrations using tip and node dating, different birth-death models, morphological clocks and combined evidence relaxed clock analyses. Customized course materials will be provided.

Software: Mesquite, TNT, RAxML, IQTree, Mr. Bayes and BEAST.

Podéis encontrar más información en https://www.transmittingscience.com/courses/evolution/morphological-phylogenetics-principles-applications-techniques/  o escribiendo a courses@transmittingscience.com  

Un cordial saludo

Sole

 

Curso online “Introduction to RNA-seq bioinformatic pipelines” del 24 al 31 de octubre, , 2023

 

Está abierta la inscripción al curso online en directo “Introduction to RNA-seq bioinformatic pipelines”.

Fechas y horario: sesiones en directo el 24, 26, 27, 30, y 31 de octubre; de 13:00 a 17:00 (zona horaria de Madrid).

Profesorado: Marcela Dotto (Instituto de Ciencias Agropecuarias del Litoral, Argentina) y Hernan G. Rosli (Instituto de Fisiología Vegetal INFIVE, Argentina).

Más información e inscripciones: https://www.transmittingscience.com/courses/genetics-and-genomics/introduction-to-rna-seq-bioinformatic-pipelines/

Resumen del curso (en inglés, que es el idioma en el que se impartirá el mismo):

This is an introductory course aiming at guiding students through the execution of the most common pipelines used to analyze different types of data generated through RNA sequencing with NGS technologies.

The course focuses on the use of Linux-based software and tools and is oriented to graduates or postgraduates with a degree in Biomedical or Life Sciences. No previous experience working with Linux-based operating systems is required.

Programme:

·      Brief introduction to Linux

·      Quality control and pre-processing of fastq files

·      SAM format and samtools

·      RNA-seq

·      Small RNA sequencing

·      LncRNA discovery

Curso online en directo: Transposable element detection using sequencing data. Del 12 al 20 de marzo, 2023.

 

Estimad@s colegas,

Está abierta la inscripción para el curso Transposable element detection using sequencing data, 2ª edición. Este curso se llevará a cabo en vivo en línea (síncrono). 

Máximo 20 participantes.

Fechas y horario: 12 al 20 de marzo, 2023. Sesiones en directo el 12, 13, 18, 19, y 20 de octubre; de 13:00 a 17:00 (zona horaria de Madrid).

Profesorado: Dra. Anna-Sophie Fiston-Lavier (Instituto de Ciencias de la Evolución de Montpellier) y Dra. Emmanuelle Lerat (Universidad Lyon 1)

Más información e inscripciones: https://www.transmittingscience.com/courses/genetics-and-genomics/introduction-to-transposable-element-detection-using-sequencing-data/ o escribiendo a courses@transmittingscience.com

RESUMEN DEL CURSO (en inglés, que es el idioma en el que se impartirà el curso)

Transposable elements (TEs) can be major components of eukaryotic genomes. Such repeated sequences, which can make up very large proportions like about 50% of mammalian genomes to more than 80% in the genomes of some plants, can promote various types of mutations, from gene interruption and expression alteration to large-scale chromosomal rearrangements. They can also promote the formation of new genes. Despite their deleterious effects, TEs are currently considered as major actors in genome evolution due the genetic and epigenetic diversity they can generate.

Even if they have a fundamental biological role, detection and analysis of TE sequences are still technologically challenging. The length and quality of sequenced reads make their detection and annotation difficult (40% detection error). Moreover, the presence of TEs in a genome can also lead to important assembly errors due to rearrangement and the merge of repeats, and to difficulties in the identification of splicing events and in the estimation of gene expression in transcriptomic analyses. It is thus important to be able to identify these sequences in genomic and transcriptomic data.

Since several years, a large number of bioinformatic tools have been developed allowing a better identification of TEs in genomes. New tools are released regularly to follow the progress of sequencing technologies but also to answer particular biological questions allowing to go from the TE annotation in assembled or unassembled genomes, to insertion polymorphism detection in natural populations. The result is a particularly large choice for users leading to difficulties in the determination of the best tool(s) to use according to the case.

In this course, we aim at proposing an introduction of selected bioinformatic tools for the detection and analysis of TEs in genomic data (RepeatMasker, DnaPipeTE, T-lex).

Vea el programa completo aquí https://www.transmittingscience.com/courses/genetics-and-genomics/introduction-to-transposable-element-detection-using-sequencing-data/#program  

Un saludo

Sole

Curso online en directo: Modelling and Analysing Multivariate Traits Evolution using mvMORPH, del 15 al 26 de mayo, 2023.

Ya está abierta la inscripción para el curso de Transmitting Science “Modelling and Analysing Multivariate Traits Evolution using mvMORPH”- 3ª edición. Max 16 participantes.

 

Fechas y horario: Online live sessions on May 15th, 17th, 22nd, 24th, and 26th; 14:00 to 16:30 and 17:00 to 19:00 (zona horaria de Madrid).

 

Profesor: Dr. Julien Clavel (NNRS, France).

 

Idioma: Inglés.

 

Resumen del curso (en inglés, que es el idioma en el que se impartirá el curso):

In this workshop students will be introduced to multivariate phylogenetic comparative methods with the mvMORPH R package.

The mvMORPH package contains tools for modelling the evolution of correlated continuous traits (e.g. morphometric measurement, geometric morphometric datasets, life history traits, gene expression data, etc.) on phylogenetic trees [ with either fossil species, extant species or both] as well as statistical tools such as multivariate generalized least squares (GLS) linear models -e.g. multivariate regression, MANOVA, MANCOVA – for studying comparative datasets.

In this course, students will be first introduced to some theory with illustrative examples (both from simulated data as well as students’ own datasets) and will learn how to interpret the models, their parameters, as well as how to assess their reliability.

Para más información piodéis chequear la página web del curso: https://www.transmittingscience.com/courses/evolution/modelling-and-analysing-multivariate-traits-evolution-using-mvmorph/ o escribir a  courses@transmittingscience.com

Curso Introducción a la Filogenómica, 1-9 octubre, ONLINE

Estimad@s colegas,

Ya está abierta la inscripción para el curso de Transmitting INTRODUCTION TO PHYLOGENOMICS – 2nd edition. Debido a las restricciones para viajar causados por la pandemia de COVID-19 este curso se impartirá en directo online.

Fechas: 1-9 de octubre, 2020.

Profesorado: Jeremy M Brown (Louisiana State University, USA) y Robert Thomson (University of Hawaii, USA).

Resumen del curso (en inglés, que es el lenguaje en el que se impartirá el curso):

 

This workshop will introduce participants to the theory and tools for phylogenetic inference in the era of genome sequencing. Course material will focus on statistical methods for phylogeny estimation, software implementing these methods, applications of these methods to large molecular datasets, and discuss trade-offs and tools for improving the accuracy of phylogenomic analyses. In hands-on practical sessions, participants will gain experience working with bioinformatic and statistical tools for analyzing large datasets.
The course is intended to facilitate ongoing or planned phylogenomics projects by students, so they are encouraged to notify instructors in advance about the topics of greatest relevance to their own work.
Example software: RevBayes, IQTree, SVDQuartets, ASTRAL, TreeScaper


Más información e inscripciones: https://www.transmittingscience.com/courses/evolution/introduction-to-phylogenomics/ o escribiendo a courses@transmittingscience.com

Un cordial saludo

Sole

LMs4TNT: Java tool to convert xy coordinates to a TNT data block

I am glad to make available a Java program that reads “x, y” coordinates of landmarks and semilandmarks from each specimen (tps or row format), estimates means for each group, and writes blocks of terminal names and the coordinates with the corresponding commands as required by TNT phylogenetic software.

You can download "jt4tnt.class" at the following URL:

http://www.filogenetica.org/Java_tool/lms4tnt.htm

Please note that “jt4tnt.class” is a java tool, thus it is platform independent. This program requires Java 6 or later (Java 1.6). Runs from your system command window writing a command line with several expressions separated by a space.

As an example, the following command line will read 300 configurations in a tps file “my300configs.tps”, will calculate means for 10 groups according to the labels in “membership10spp.txt”, and will write these in the output file “my10spp.txt” with all necessary TNT commands:

>java jt4tnt -i my300configs.tps -o my10spp.txt -m membership10spp.tx

There is more info on examples, input data file formats, membership list file, and output files in the website.

I guess you can cite this tool as:
Sandria, J. & E. De Luna. LMs4TNT, Java tool to convert xy coordinates to a TNT data block. jt4tnt v1.0, jan/21/2016. url: http://www.filogenetica.org/Java_tool/lms4tnt.htm (date accessed: xxxxxxx).

Curso de Filogenia y Morfometría Geométrica en Barcelona

Ya está abierta la inscripción para la 9ª edición del curso de Transmitting science "Geometric Morphometrics and Phylogeny "

Fechas: Del 9  al 13 de septiembre de 2019

Profesor:  Dr. Chris Klingenberg (University of Manchester, United Kingdom)

Lugar: Capellades, Barcelona (España)

Más información y matrícula:

https://www.transmittingscience.org/courses/geometric-morphometrics/geometric-morphometrics-phylogeny/

Programa del curso:

 

1. Phylogeny, trees and phylogenetic reasoning.

2. Brief review of geometric morphometrics (Procrustes fit, PCA, etc.).

3. Mapping traits onto phylogenies: squared-change parsimony.

4. Practice: making/editing Nexus files, mapping morphometric data onto the tree (Mesquite, MorphoJ).

5. Phylogenetic signal, morphometric traits and estimating phylogeny.

6. Comparative methods: independent contrasts.

7. Application in morphometrics: evolutionary allometry and size correction.

8. Practice: comparative methods (MorphoJ).

9. Application of comparative methods: morphological integration.

10. Multi-level analyses of integration: inferring evolutionary mechanisms.

11. Application of comparative methods: partial least squares (ecomorphology, etc.).

12. Practice: comparative methods (cont.).

13. Morphometrics, phylogenies and qualitative characters.

14. Disparity and diversification.

15. Presentations of group work.

Reunión Argentina de Cladistica en Tucumán, 2019

XII Reunión Argentina de Cladistica y Biogeografía,
8-10 de Abril, 2019,
San Miguel de Tucumán, Argentina.

Curso de Análisis filogenéticos con R - del 3 al 7 de Septiembre, 2018 Barcelona.

Ya está abierta la inscripción al curso" Phylogenetic Analysis Using R – 5ª edición"; del 3 al 7 de septiembre, 2018.

Profesores: Dr. Emmanuel Paradis (Institut de Recherche pour le Développement, France) y Dr. Klaus Schliep (University of Massachusetts Boston, United States of America)

Web e inscripciones: http://www.transmittingscience.org/courses/phylogeny/phylogenetic-analysis-using-r/

Este curso se centra en el análisis de secuencias moleculares múltiples en varios niveles: poblaciones, especies, comunidades y clados. Durante el curso se abordarán cuestiones sobre las relaciones evolutivas entre estas secuencias, así como la evolución de la biodiversidad a diferentes escalas.

Los objetivos principales del curso son: (i) aprender a distinguir estrategias de análisis de datos moleculares a nivel inter- o intraespecífica, (ii) ser capaces de iniciar un análisis filogenético a partir de los archivos de secuencias moleculares, la interpretación de los resultados y los gráficos obtenidos.

Además se enseñará la aplicación de paquetes estadísticos de R especializados en este tipo de análisis. En particular ape, phangorn, y adegenet.

Para este curso se requieren conocimientos previos en estadística multivariante, filogenias y evolución molecular así como un nivel usuario de estadística con R.