• Advanced Courses in Life Sciences

    Header of Evolution at Transmitting Science

7th Edition

Phylogenetic Analysis Using R

August 24th-28th, 2020

Evolution

Evolution

This course will be delivered ONLINE: 20 hours of online live lessons,  plus 15 hours of recorded classes and assignments. A good internet connection is required to follow the course.

Phylogenetic Analysis Using R

Course overview

This course is for biologists dealing with the analysis of multiple molecular sequences at several levels: Populations, species, clades, communities. These biologists address questions relative to the evolutionary relationships among these sequences, as well as the evolutionary forces structuring biodiversity at different scales.

The objectives of the course are: (i) to know how to choose a strategy of molecular data analysis at the inter‐ or intraspecific levels, (ii) to be able to initiate a phylogenetic analysis starting from the files of molecular sequences until the interpretation of the results and the graphics.

The software used for this course will be centered on the R language for statistics. This will include the use of specialized packages particularly ape, phangorn, and adegenet.

REQUIREMENTS

Graduate or postgraduate degree in any Biosciences discipline. Knowledge of multivariate statistics, phylogenetics and molecular evolution. User level of R.

All participants must have a personal computer (Windows, Macintosh), with webcam if possible, and a good internet connection.

Contact

courses@transmittingscience.com

LOCATION

This course will be delivered online.

Please check the schedule for the live online part, and be aware that it is GMT+1.

DATE

August 24th-28th, 2020

LANGUAGE

English

COURSE LENGTH & ECTS

35 hours online.

This course is equivalent to 2 ECTS (European Credit Transfer System) at the Life Science Zurich Graduate School.

The recognition of ECTS by other institutions depends on each university or school.

PLACES

Places are limited to 16 participants and will be occupied by strict registration order.

Participants who have completed the course will receive a certificate at the end of it.

Emmanuel Paradis instructor for Transmitting Science

Dr. Emmanuel Paradis
Institut de Recherche pour le Développement
France

Klaus Schliep instructor for Transmitting Science

Dr. Klaus Schliep
University of Massachusetts Boston
United States of America

Program

Monday: Phylogenetic data with R.

  • Morning: Basics on phylogenetic data (sequences, alignments, trees, networks, “splits”) and other data in R. Reading / writing data from files or from internet. Matching data. Manipulating labels. Subsetting data.
  • Afternoon: Applications.

Tuesday: Managing sequences.

  • Morning: Theory of sequence alignment. Comparing alignments. Graphical analyses of alignments.
  • Afternoon: Applications.

Wednesday: Phylogenetic reconstruction with distance-based methods.

  • Morning: Theory and methods of phylogeny reconstruction. Comparison of methods. The variance of distances. Distance-based methods: General principles and the main methods (NJ, BIONJ, FastME, MVR). Methods for incomplete distances matrices (NJ*, BIONJ*, MVR*). Methods for combining several matrices (SDM). Parsimony methods.
  • Afternoon: Applications.

Thursday: Phylogenetic reconstruction with maximum likelihood methods.

  • Morning: Theory of maximum likelihood and application to phylogeny reconstruction. Substitution models. Tree space and topology estimation. Introduction to the package phangorn.
  • Afternoon: Applications.

Friday: Tree space and tree comparison.

  • Morning: Tree comparison, consensus methods, topological space and distances, bootstrap and Bayesian methods.
  • Afternoon: Applications.

Literature

  • Felsenstein J (2004) Inferring phylogenies, Sunderland: Sinauer Associates.
  • Lemey P, Salemi M and Vandamme A-M (2009) The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing (Second Edition), Cambridge: Cambridge University Press.
  • Paradis E (2012) Analysis of Phylogenetics and Evolution with R (Second Edition), New York: Springer.

Fees

You can check the list of Ambassador Institutions. If you want your institution to become a Transmitting Science Ambassador please contact us at communication@transmittingscience.com

Funding

Discounts are not cumulative and apply only on the Course Fee. We offer the possibility of paying in two instalments (contact courses@transmittingscience.com).

Former participants will have a 5 % discount on the Course Fee.

20 % discount on the Course Fee is offered for members of some organizations (Ambassador Institutions). If you want to apply to this discount please indicate it in the Registration form (proof will be asked later).

Unemployed scientists living in Spain, as well as PhD students based in Spain without any grant or scholarship to develop their PhD, could benefit from a 40 % discount on the Course Fee. If you want to ask for this discount, please contact the course coordinator. That would apply for a maximum of 2 places and they will be covered by strict inscription order.