• Theoretical knowledge of basic concepts of evolution and molecular epidemiology.
  • Storing information: databases
  • Exploring and using public systems of sequence similarity database searching.
  • Sequence alignment
  • Phylogenetic trees


  • To know the fundamental evolutionary concepts used in Public Health.
  • To know how to use the most important public systems for data search.
  • To know how to make alignments and phylogenetic trees of genomic sequences.
  • To be able to analyse the obtained information in the context of Public Health.


  • To be able to use the bibliographic, methodological and technological resources to solve a scientific problem using bioinformatics.

General characterization





Responsible teacher

Ana Barroso Abecasis, Isabel Cristina Maciel Natário


Weekly - Available soon

Total - 41

Teaching language





Arthur M. Lesk. Introduction to Bioinformatics. 3rd Ed. 2008. Oxford University Press.

Philippe Lemey, Marco Salemi and Anne-Mieke Vandamme. The Phylogenetic Handbook – A Practical Approach to Phylogenetic Analysis and Hypothesis Testing. 2009. Cambridge University Press.

Teaching method

The course will have theoretical classes, practical classes, journal clubs and classes to assist in the development of the final project. The students will be frequently challenged to do literature search, especially for the journal club classes and for the development of the final project.

Evaluation method

The final grade will have a component based on the programme taught, based on the students’ performance in the practical classes (25%) and on the final exam grade (25%); and a component based on the final project (50%).

The final project consists on a scientific study, in which the students should develop a methodology to investigate a scientific problem that requires bioinformatics methods to be solved. Each student should ideally select his own scientific problem. The teacher will provide guidance to the students in ‘guiding classes’ during the development of the project.

Subject matter

1. Theoretical knowledge of basic concepts of evolution and molecular epidemiology

1.1 The genetic code

1.2 Mutations: transitions and transversions

1.3 Evolutiona and mutations fixationsEvolução e fixação de mutações

1.4 Selective pressurePressão selectiva

1.5 Evolutionary models: stochastic and deterministic

1.6 Evolutionary rate

1.7 Molecular clock


2. Storing information: databases

2.1 Primary vs Secondary databases

2.2 Literature search and organizing information

2.3 Databases of nucleotide sequences

2.4 Databases of aminoacid sequences


3. Sequence alignments

3.1 Homology vs Similarity

3.2 Definition of Alignments

3.3 Types of alignments

3.3.1 Pairwise alignments: BLAST

       3.3.2 Multiple alignments

       3.3.3 Local vs Global alignments

3.4 Nucleotide vs Aminoacid alignments

3.5 Practical exercises


4. Phylogenetic trees

              4.1 Definition of phylogenetic trees

              4.2 Rooted and unrooted phylogenetic trees

              4.3 Monophyly vs Paraphyly

              4.4 Methods to estimate phylogenetic trees

              4.5 Estimating tree and clustering reliability

              4.6 Practical exercises


Programs where the course is taught: