Practical Course on Phylogenetics

Practical Course on Phylogenetics

  • Lecturer(s) or Responsible(s): Octávio Paulo (DBA professor, cE3c researcher)
  • Department Responsible: Departamento de Biologia Animal (FCUL)
  • Data: January 28th, 2019 to February 1st, 2019
  • Deadline for Applications: January 11th, 2019
  • Duration: 36 hours
  • Schedule: 13h-20h, Monday-Thursday; 13h-21h Friday
  • Nº (min, max) Students: 15-20
  • Location: Room 2.3.16, Building C2, Faculdade de Ciências da Universidade de Lisboa, Campo Grande 1749-016 Lisboa


Phylogenetics is one of the scientific areas of Biology that has grown fast and evolved in methodological terms in the last years. Its applications go from the studies of the evolution of species and populations to the least expected, as the study of the origin of the AIDS virus or seasonal cycles of the flu. The course is aimed at students and professionals that intend to get started in phylogenetic analysis as well as researchers already with some experience wanting to deepen or update their knowledge in the field. The course consists of theoretical classes as well as hands-on practical sessions using software. Participants are encouraged to bring their own sequence data for analysis.

This course can have a recognition of 6 ECTs for FCUL PhD students enrolling in it as part of their first doctoral year. For FCUL PhD students only requiring 5 ECTs recognized in their specific PhD programmes the last 6 hours of the course are not mandatory and the certificate will be on 'Topics in Phylogenetics’.

Minimum formation: students of ‘Licenciatura’ (bachelor) in Biology

Directed to: PhD or MSc students in Biology, Evolution, Ecology or related areas, postdocs and professionals working in related topics

General Plan


Brief historic perspective about phylogenetics and molecular evolution. Review of the basic concepts regarding genome organization, structure and function of genes, genetic codes and mutation types.

Basic principles of phylogenetic analysis: character evolution, homologies and homoplasies, evolutionary tree types, types of data sets for analysis etc.

Methods of phylogenetic inference: parsimony, distances, maximum likelihood and Bayesians. Models of molecular evolution. Substitution rates and patterns. Methods of model selection. Search algorithms and optimization solutions. Exhaustive and heuristic searches. Analysis of the robustness of phylogenetic trees and their components. Hypothesis testing on evolutionary trees.


Students fees.




Free for 1st year PhD students in the Doctoral programme in Biology (UL), Biodiversity, Genetics and Evolution (UL; UP) and Biology and Ecology of Global Changes (UL; UA) when the course counts credits for their formation, in which case the delivery of a final report done after the course is mandatory; 300 euros for Professionals and postdocs, 250 euros for  BTI, BI and PhD students  and  180 euros for master and bachelor students in FCUL as well as unemployed

When the maximum number of students is reached 10 vacancies will be available for non-paying 1st year PhD students mentioned above, being, by order of preference: 1) cE3c students; 2) BIODIV students (not from cE3c); 3) FCUL students (not from cE3c); 4) BEAG students (not from FCUL).

How to apply

To apply send an e-mail to with the following information:




Professional activity:  Professional/Postdoc

BTI, BI, PhD student (with/ without scholarship)  Lic./Master student

Academic formation:


Student of the 1st year of Doctoral programme Biodiv (FCUL/FCUP), Biologia (FCUL) or BEAG (FCUL or UA)?: