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Advanced Courses in Life Sciences

5th Edition

Phylogenetic Analysis Using R

September 3rd-7th, 2018, Barcelona (Spain)


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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.


Institut Català de Paleontologia Miquel Crusafont (ICP)

C/ de l’Escola Industrial, 23
08201 Sabadell, Barcelona (Spain)

How to get there


September 3rd-7th, 2018




35 hours on-site.

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

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


Places are limited to 20 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

Klaus Schliep instructor for Transmitting Science

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


Ana Rosa Gómez-Cano coordinator at Transmitting Science

Dr. Ana Rosa Gómez-Cano
Transmitting Science

Soledad De Esteban-Trivigno instructor at Transmitting Science

Dr. Soledad De Esteban-Trivigno
Transmitting Science


Graduate or postgraduate degree in any Biosciences discipline. Knowledge of multivariate statistics, phylogenetics and molecular evolution. User level of R. All participants must bring their own personal laptop (Windows, Macintosh, Linux).


Monday, September 3rd, 2018. 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, September 4th, 2018. Managing sequences.

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

Wednesday, September 5th, 2018. 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, September 6th, 2018. 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, September 7th, 2018. Tree space and tree comparison.

  • Morning: Tree comparison, consensus methods, topological space and distances, bootstrap and Bayesian methods.
  • Afternoon: 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
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  • Early bird (until May 31st, 2018):
  • 575
  • Regular (after May 31st, 2018):
  • 720
  • This includes course material, coffee breaks and lunches (VAT included).

We offer the possibility of paying in two instalments (contact the course coordinators).


The course will take place in the city of Sabadell, Barcelona (Spain). Take a look at the venue.

You may stay in Barcelona city or Sabadell. You will find information about Hotels and Hostel in Sabadell here. It takes about 45 minutes by public transport to arrive to Sabadell from the centre of Barcelona city. The place of the course is about 15 minutes walking from the train stop.


Course Schedule
  • Monday to Friday:
    • 9:30 to 13:30 Lessons.
    • 13:30 to 15:00 Lunch (included).
    • 15:00 to 18:00 Lessons.



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

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

Spanish unemployed scientists, as well as Spanish PhD students 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 coordinators. That would apply for a maximum of 2 places and they will be covered by strict inscription order.

Discounts are not cumulative and apply only on the fee, not to Accommodation Package or other options.


You will find below some testimonials from former participants to previous editions of this course:

Margherita Montalbano Di Filippo

“This course was fantastic! It is a must for those who want to make phylogenetic analysis and implement that knowledge in R. The instructors help you understand how to use certain analyses associated to your data. Congratulations to the organizer, everything was perfect! It truly was an amazing experience meeting the instructors, as well as interacting and making new friends with the other students. It was a great week filled with many memories that I can honestly say that I would definitely do another course in future.” (4th Edition)

Margherita Montalbano Di FilippoUniversity of Rome Tor Vergata, Italy
Dr. Susanna López-Legentil

“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 and what you can do and cannot do (mostly ‘can’, as with R it is all a matter of writing new functions / commands to get your answers!). I enjoyed this course thoroughly and I will certainly apply all I have learned to my current research!” (1st Edition)

Dr. Susanna López-LegentilUniversitat de Barcelona, Spain

Previous editions of this course

4th Edition, March 6th-10th, 2017

Course Phylogenetic Analysis Using R - 4th Edition, March 6th-10th, 2017Twenty-one people belonging to the following countries and institutions participated in this edition:

  • Italy: University of Rome Tor Vergata.
  • Germany: Justus Liebig University.
  • Spain: Lifesequencing, Universidad de Salamanca, Centro Nacional de Microbiología – Instituto de Salud Carlos III.
  • United States of America: University of Wisconsin – Madison.
  • France: Institut de Génomique Fonctionnelle de Lyon – CNRS, Station Biologique de Roscoff – CNRS.
  • Israel: Bar-Ilan University.
  • Portugal: Universidade do Porto.
  • Turkey: Karadeniz Technical University.
  • Sweden: Lund University, Biomedical Center – Uppsala University, University of Gothenburg.
  • The Netherlands: Wageningen University.
  • United Kingdom: University of Nottingham.
  • Poland: University of Lodz.
  • Algeria: Annaba University.
  • Norway: University of Oslo, NTNU University Museum.

3rd Edition, January 25th-29th, 2016

Course Phylogenetic Analysis Using R - 3rd Edition, January 25th-29th, 2016Thirteen people belonging to the following countries and institutions participated in this edition:

  • Sweden: Lund University.
  • Spain: Universidad Rey Juan Carlos.
  • Brazil: Universidade de São Paulo, Museu de Zoologia da Universidade de São Paulo.
  • United Kingdom: University of Cambridge, Royal Botanic Gardens – Kew, University of Hull.
  • United States of America: University of Wisconsin – Madison.
  • Belgium: Ghent University.
  • Poland: Wrocław University of Environmental and Life Sciences.
  • The Netherlands: Stichting HIV Monitoring.

2nd Edition, May 4th-8th, 2015

Course Phylogenetic Analysis Using R - 2nd Edition, May 4th-8th, 2015Twenty people belonging to the following countries and institutions participated in this edition:

  • Brazil: Federal University of São Carlos.
  • Poland: Institute of Nature Conservation – Polish Academy of Sciences, University of Gdańsk.
  • Denmark: Natural History Museum of Denmark – University of Copenhagen.
  • Germany: Philipps-Universität Marburg, Research Center Borstel, University of Rostock.
  • United Kingdom: Plymouth University, Royal Botanic Gardens – Kew.
  • Slovakia: Technical University in Zvolen.
  • Spain: Universidad de Sevilla.
  • Portugal: Universidade de Évora.
  • South Africa: University of Cape Town.
  • Switzerland: University of Fribourg.
  • Italy: University of Pisa.
  • Sweden: Uppsala University.
  • The Netherlands: Wageningen University.

1st Edition, April 15th-19th, 2013

Course Phylogenetic Analysis Using R - 1st Edition, April 15th-19th, 2013Eighteen people belonging to the following countries and institutions participated in this edition:

  • Austria: University of Innsbruck, University of Vienna.
  • Spain: Universitat de Barcelona, Universidad de Granada, University of Cadiz.
  • The Netherlands: Plant Research International, Wageningen University.
  • Belgium: Ghent University, University of Antwerp.
  • Norway: University of Oslo.
  • Italy: University of Pisa.
  • Switzerland: University of Lausanne.
  • Indonesia: Bogor Agricultural University.


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