The aim of this course is to understand the main concepts and methodologies in comparative and functional genomics.

  • Introduce the main comparative approaches to ascertain the evolution of genes and complete genomes, covering genome wide analyses of gene gains, losses, duplications and gene order conservation.
  • This will be complemented by learning about phylogenomics analyses and the information obtained from widespread phylogenetic reconstruction.
  • A third part of the course will focus on the functional characterization of unknown proteins using different tools based on comparative genomics and differential gene expression.

Final Project

  • Project


Blast database

Species tree

Journal Club

  • Journal Club



Session 1. Genes and their functions

  • Lecture

Lesson 1


Session 1. Introduction to databases and homology-based functional inference

  • Practical

Practical Lesson 1

Exercises Lesson 1

Data 1

Data 2

Data 3


Session 2. Comparative sequence analysis

  • Lecture

Lesson 2


Session 2. Orthology assignment

  • Practical

Practical Lesson 2

Exercises Lesson 2


Exercise Data



Session 3. Phylogenetic analyses

  • Lecture

Lesson 3


Session 3. Sequence based functional annotation

  • Practical

Practical Lesson 3

Command line

Command line - solved

Exercises Lesson 3

Exercise Data


Session 4. Phylogenomics

  • Lecture

Lesson 4


Session 5. Genome comparisons and evolution of gene order

  • Lecture

Lesson 5


Session 5. Phylogenetics and phylogenomics

  • Practical

Practical Lesson 5

Exercices Lesson 5

Exercise Data



Session 6. Phylogenetic profiling and co-evolution

  • Lecture

Lesson 6


Session 6. Gene Order

  • Practical

Exercices Lesson 6



Session 7. Gene expression analysis

  • Lecture

Lesson 7


Session 8. Comparative and Functional analysis of genomes

  • Lecture

Lesson 8


Session 8. Differential expression analysis

  • Practical

Practical Lesson 8

Exercise Data

Exercices Lesson 8