• Advanced Courses in Life Sciences

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Online Course – 9th Edition

Phylogenetic Analysis Using R

July 18th-22nd, 2022

This course will be delivered live online

25 hours of online live lessons plus 5 hours of exercises to do between the live sessions

Live sessions will be recorded. Recordings will be made available to participants for a limited period of time. However, attendance to the live sessions is required.


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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.


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.




July 18th-22nd, 2022

Schedule and Course length

Online live sessions from Monday to Friday  (Madrid time zone)

    • 13:00-15:30 – Live session
    • 15:30-16:00 – Break
    • 16:00-18:30 – Live session

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

This course is equivalent to 1 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 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.

Testimonials for this course

Phylogenetic Analysis using R (onsite) – 4th edition

“This course was fantastic! It is a must for those who want to make phylogenetic analysis and implement that knowledge in R. Everything was perfect! It truly was an amazing experience meeting the instructors, as well as interacting and making new friends with the other students.”

Phylogenetic Analysis using R (onsite) – 1st edition

“This course is a ‘must’ for any researcher working on phylogenetics. The instructors do an outstanding job of explaining the potential of the available packages. I enjoyed this course thoroughly and I will certainly apply all I have learned to my current research!”

Phylogenetic Analysis using R (online) – 7th edition

“What I enjoyed most (and what gave me most improvements) was the chance to see the lecturers really scripting live, as it also showed me how this is done by professionals (including some tiny tricks or better way of “programming behaviour” totally aside of the topic of the course). Also the possibility of Q&A was awesome.”

Emmanuel Paradis instructor for Transmitting Science

Dr. Emmanuel Paradis
Institut de Recherche pour le Développement

Klaus Schliep instructor for Transmitting Science

Dr. Klaus Schliep
Graz University of Technology

Haris Saslis coordinator for Transmitting Science

Dr. Haris Saslis
Transmitting Science


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.


  • 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 Fee
  • Early bird (until June 30th, 2022):
  • 536 €
    (428.8 € for Ambassador Institutions)
  • Regular (after June 30th, 2022):
  • 596 €
    (476.8 € for Ambassador Institutions)
  • The price is VAT included.
    After registration you will receive confirmation of your acceptance in the course. Payment is not required during registration.

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


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 may benefit from a 40 % discount on the Course Fee. If you would like to enquire about this discount, please contact the course coordinator. That would apply for a maximum of 2 places and they will be covered by strict registration order.