DETAILED PROGRAM
[ Day 1: the ice-breaker day ]
Tuesday 6th of June
14:00 - 14:15
Welcome to the ITA*PHY workshop!
[ Organisers ]
14:15 - 15:15
A brief introduction to the command line interface and BASH
[ Giobbe and Jacopo ]
15:15 - 15:30
Coffee break
[ All ]
15:30 - 17:00
Flash talks: max 5 min. and 1 slide per person (3 minutes talk + 2 minutes feedback from instructors and participants) (pt. 1)
[ Participants ]
17:00 - 17:10
Coffee break
[ All ]
17:10 - 18:35
Flash talks: max 5 min. and 1 slide per person (3 minutes talk + 2 minutes feedback from instructors and participants) (pt. 2)
[ Participants ]
18:40 - 20:30
Final break and (almost) practical lecture: the evolution of the aperitif with (alcoholic and non-alcoholic) drinks
[ Omar ]
[ Day 2: the error day ]
Wednesday 7th of June
09:00 - 09:50
Practical lecture: dataset preparation in phylogenomics 1 (how to download, clean, format, align and trim sequence data)
[ Andrea ]
09:50 - 10:40
Practical lecture: dataset preparation in phylogenomics 2 (orthology inference and multi-gene datasets)
[ Giobbe and Jacopo ]
10:40 - 11:00
Coffee break
[ All ]
11:00 - 12:15
Practical lecture: Maximum likelihood phylogenetic analysis with IQTree
[ Giobbe and Jacopo ]
12:15 - 13:30
Lunch break
[ All ]
13:30 - 15:30
Theoretical lecture: Systematic errors in phylogenomics
[ Omar and Giobbe ]
15:30 - 16:00
Coffee break
[ All ]
16:00 - 18:00
Practical lecture: Bayesian phylogenetic analysis with BEAST
[ Omar, Nicola and Andrea ]
18:00 - 18:30
Open discussion
[ All ]
19:30 - 22:00
Social: walk and aperitif/dinner in Trento
[ All ]
[ Day 3: the gene-tree day ]
Thursday 8th of June
08:30 - 10:00
Theoretical lecture: Species tree inference from genome scale datasets
[ Benoît ]
10:00 - 10:15
Coffee break
[ All ]
10:15 - 11:45
Theoretical lecture: Gene tree - species tree reconciliation
[ Benoît ]
11:45 - 12:15
Round table: Species trees and gene trees
[ All ]
12:15 - 13:15
Lunch break
[ All ]
13:15 - 15:15
Practical lecture: Species tree inference from genome scale datasets
[ Benoît ]
15:15 - 15:30
Coffee break
[ All ]
15:30 - 17:30
Practical lecture: Gene tree - species tree reconciliation
[ Benoît ]
18:30 - 23:30
Social: Aperitif + round table in Sardagna (click here to get the location of the cable car station) and course dinner at 8:30 pm @Ristorante/Pizzeria Rosa d'oro
[ All ]
[ Day 4: the clock day ]
Friday 9th of June
09:00 - 10:30
Theoretical lecture: Bayesian phylogenomic dating
[ Sandra ]
10:30 - 11:00
Coffee break
[ All ]
11:00 - 12:30
Theoretical lecture: MCMC: mixing, convergence, and efficiency
[ Sandra ]
12:30 - 13:00
Round table: Bayesian dating using genome-scale data
[ All ]
13:00 - 14:00
Lunch break
[ All ]
14:00 - 16:00
Practical lecture: guided practical to use PAML for phylogenomic dating analyses (part I)
[ Sandra ]
16:00 - 16:30
Coffee break
[ All ]
16:30 - 18:30
Practical lecture: guided practical to use PAML for phylogenomic dating analyses (part II)
[ Sandra ]
18:30 - 19:00
Round Table: wrap up and feedback from students
[ All ]
19:00 - 22:00
Social: walk and aperitif/dinner in Trento
[ All ]
[ Extra: the MUSE day ]
Saturday 10th of June
Important notice: coffee breaks, Tuesday aperitif and course dinner are covered, but not housing or food on the other days.