Programme – tentative and subject to change


Day 1 (Sunday 10th January) “Meet and Greet”

20:00 22:00 Meeting with Students and refreshments (All teachers)

 

Day 2 (Monday 11th January) “Setting the Scene and preparing the data”

09:00 11:00 Lecture I: “Introduction to Gene and Genome Evolution, searching tree space and determining support” – Prof. James McInerney
11:00 11:15 Coffee Break
11:15 12:30 Practical Session I: Introduction to Linux for bioinformatics analyses – Dr. Chris Creevey (leading demonstrator)
12:30 14:00 Lunch Break
14:00 15:30 Practical Session II : “Sequence alignments: how do I get it right?” – Dr. Karen Siu Ting/Dr. Claire Morgan
15:30 15:45 Coffee Break
15:45 17:00 5-Alive Student presentations (5 mins, 5 slides).
17:00 17:45 Research Seminar: Dr. Claudia Russo
19:00 21:00 Dinner

 

Day 3 (Tuesday 12th January) “Single Gene Analyses”

09:00 11:00 Lecture II: “Introduction to Maximum Likelihood and the assessment of phylogenetic hypotheses” – Dr Mark Wilkinson
11:00 11:15 Coffee Break
11:15 12:30 5-Alive Student presentations (5 mins, 5 slides).
12:30 14:00 Lunch Break
14:00 15:30 Practical Session III: “PAUP and Raxml Maximum Likelihood I” – Prof James McInerney + All teachers  (leading demonstrators)
15:30 15:45 Coffee Break
15:45 17:00 Practical Session IV: “PAUP and Raxml Maximum Likelihood II”– Prof James McInerney + All teachers (leading demonstrators)
17:00 17:45 Research Seminar: Dr. Chris Creevey
19:00 21:00 Dinner

 

 Day 4 (Wednesday 13th January) “Complex models of Evolution”

09:00 11:00 Lecture III: “Bayesian phylogenetics and heterogeneous models of evolution” – Dr. Omar Rota Stabelli
11:00 11:15 Coffee Break
11:15 12:30 Practical Session V: “MrBayes & Phylobayes – Bayesian phylogenomics and estimation of divergence times” – Dr. Omar Rota Stabelli
12:30 14:00 Lunch Break
14:00 15:30 Practical Session VI:  “Heterogeneous Maximum Likelihood using P4 I” – Dr. Claire Morgan (leading demonstrator)
15:30 15:45 Coffee Break
15:45 17:00 Practical Session VII:   “Heterogeneous Maximum Likelihood using P4 II” – Dr. Claire Morgan (leading demonstrator)
17:00 17:45 Research seminar: Dr. Mary O’Connell
19:00 21:00 Dinner

 

Day 5 (Thursday 14th January) Multiple gene analyses

09:00 11:00 Lecture IV: “Large-scale phylogenetic analyses: supertrees & supermatrics” – Dr. Mark Wilkinson
11:00 11:15 Coffee Break
11:15 12:30 Practical Session VIII: “Unix pipelining and the automation of analyses in comparative genomics and phylogenomics” – Dr. Chris Creevey (leading demonstrator)
12:30 14:00 Lunch Break
14:00 15:30 Lecture V: “Large-scale selective pressure analysisPractical Session IX: Genome-scale analysis of selection using PAML – Dr. Mary O’Connell (leading demonstrator)
15:30 15:45 Coffee Break
15:45 17:45 Practical Session X: Genome-scale analysis of selection using PAML – Dr. Mary O’Connell (leading demonstrator)
17:00 17:45 Research Seminar: Dr. Omar Rota Stabelli
19:00 21:00 Dinner

 

Day 6 (Friday 15th January) “Scaling up”

09:00 11:00 Group Time
11:00 11:15 Coffee Break
11:15 12:30 Practical Session XI:“Gene-tree / Species-tree reconciliation” – Dr. Chris Creevey (leading demonstrators)
12:30 14:00 Lunch Break
14:00 15:30 Practical Session XII: “Assessing phylogenetic hypotheses – A problem based approach” – Dr. Karen Siu Ting + All teachers (Leading Demonstrators).
15:30 15:45 Coffee Break
15:45 17:00 Practical Session XIII: “Identifying rogue taxa in phylogenomic datasets” – Dr. Karen Siu Ting + All teachers (Leading Demonstrators).
17:00 17:45 Research Seminar: Dra Carmen Rosa García Dávila
19:00 21:00 Dinner

 

Day 7 (Saturday 16th January) “Integrating diverse data types”

09:00 11:00 Practical Session XIV: “Phylogenomic analyses from transcriptome data I” – Dr. Chris Creevey (Leading Demonstrators).
11:00 11:15 Coffee Break
11:15 12:30 Practical Session XV: “Phylogenomic analyses from transcriptome data II” – Dr. Chris Creevey (Leading Demonstrators).
12:30 14:00 Lunch Break
14:00 15:30 Practical Session XVI – Analysis of student’s datasets – All teachers
15:30 15:45 Coffee Break
15:45 17:00 Practical Session XVII – Analysis of student’s datasets – All teachers
17:00 17:45 Research Seminar: Prof. James McInerney
19:00 21:00 Dinner

 

Day 8 (Sunday 17th January) “Discussion and close”

09:00 11:00 Round Table Discussion I – All teachers
11:00 11:15 Coffee Break
11:15 12:30 Round Table Discussion II – All teachers
12:30 14:00 Lunch Break

 

Course Ends.