ForBio and Transmitting Science 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 apephangorn, and adegenet.



Online live sessions from Monday 19th to Friday 23rd ((GMT+2, Madrid time zone)

    • 08:00-10:30 – Morning live session
    • 10:30-11:30 – Break
    • 11:30-14:00 – Afternoon live session

Phylogenetic data with R.

  • 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.
  • Applications.

Managing sequences.

  • Theory of sequence alignment. Comparing alignments. Graphical analyses of alignments.
  • Applications.

Phylogenetic reconstruction with distance-based methods.

  • 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.
  • Applications.

Phylogenetic reconstruction with maximum likelihood methods.

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

Tree space and tree comparison.

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

Recomended reading

  • 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.

Course duration: 30 hours, 25 hours live online and 5 hours of exercises between the live sessions.


     Dr. Emmanuel Paradis, Institut de Recherche pour le Développement, France
     Dr. Klaus SchliepUniversity of Massachusetts Boston, United States of America

Coordinator: Hugo de Boer ( – ForBio. 

Credits: A 1 ECTS course certificate will be given to students that pass the course.

Level: 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.

Participants: Maximum 16.

Application deadline: April 30th, 2021 (For ForBio members).

Fee: ForBio has a limited number of course waivers for this course for ForBio members (MSc and PhD students, and postdocs). ForBio associates can get a 20% discount on the course fee.

Click here for more information about the course.

For those interested in registering in this course, please do so through the Transmitting Science website

Published Jan. 4, 2021 3:05 PM - Last modified Jan. 4, 2021 3:05 PM