9:30-9:45 am      Introduction and welcome (James McInerney) [ website ]
9:45-10:30          Seminar 1 (James McInerney): Multiple alignment - why and how [ ppt ]
10:30-11:45        Seminar 2 (Alberto Dávila): Genomics Analyses Resources for Sequence Annotation [GARSA] [ ppt ]
11:45-1:30          Lunch
1:30-3:30            Practical session I (GARSA) [ doc ]
3:30-3:45            Coffee break
3:45-4:30            Seminar 3 (Erik Sonnhammer) : Fast multiple alignments with KAlign [ ppt ]
4:30-5:30            Seminar 4  (Maria Claudia Cavalcanti) : In silico workflows [ ppt ]

8:30-10:15      Lecture 1 (Ann-Charlotte Sonnhammer): Orthology analyses [ ppt ]
10:15-10:30    Coffee break/discussion
10:30-11:45    Practical session I (Orthology analyses) [ doc ]
11:45-1:30      Lunch
1:30-3:30        Practical session II (Orthology analyses)
3:30-3:45        Coffee break
3:45-5:00        Practical session III (Orthology analyses)

8:30-10:15 am Lecture 2 (Erik Sonnhammer): Protein domain analysis (Pfam, Interpro) and Transmembrane  topology prediction (Phobius, SFINX) [ ppt ]
10:15-10:30    Coffee break/discussion
10:30-11:45    Practical session I (Pfam, InterPro, Phobius, SFINX) [ doc ]
11:45-1:30      Lunch
1:30-3:00        Practical session II (Pfam, InterPro, Phobius, SFINX)
3:00-3:15        Coffee break
3:15-4:45        Practical session III (Pfam, InterPro, Phobius, SFINX)
4:45-5:30        Seminar 5 (Mar Albà): Gene evolutionary rate variation in metazoans

8:30-10:15 am    Lecture 3 (Mar Albà): Comparative analysis of eukaryotic genes [ website ]
10:15-10:30        Coffee break/discussion
10:30-11:45        Practical session I (Promoter sequence analysis)
11:45-1:30          Lunch
1:30-4:00            Poster presentations (with coffee)
4:00-5:00            Practical session II (Gene mining using Biomart)

8:30-10:15am    Lecture 4 (Christine Orengo): Structure comparison, structure classifications [ ppt ]  [ ppt ]
10:15-10:30       Coffee break/discussion
10:30-11:45       Practical session I (Structural classification and identifying structural relatives in the genomes)
11:45-1:30         Lunch
1:30-3:00           Practical session II (Structural classification and identifying structural relatives in the genomes)
3:00-3:15           Coffee
3:15-4:45           Practical session III (Structural classification and identifying structural relatives in the genomes)
4:45-5:45           Seminar 6 (James McInerney): The influence of horizontal gene transfer on the evolutionary history of the prokaryotes [ website ]

8:30-10:15 am Lecture 5 (James McInerney): [ website ]
1. Parsimony
2. Distance matrix methods
3. Maximum likelihood
4. Bayesian approaches
5. Confidence in data and hypothesis

10:15-10:30     Coffee break/discussion
10:30-11:45     Practical session I (Phylogenetics)
11:45-1:30       Lunch
1:30-3:30         Practical session II (Phylogenetics)
3:30-3:45         Coffee break
3:45-5:00         Practical session III (GARSA) [ doc ]
7:00                 Course dinner.