Practical Course

European Molecular Biology Organization

 

Computational molecular evolution

29 April - 10 May 2012 | Heraklion | Greece

Programme

 

Day 0
( Sunday, 29 April 2012)
 
    Participants check in at the hotel in Gouves
     
Day 1
(Monday, 30 April 2012)
 
  09.00 - 10.15 Introductions
Giorgos Kotoulas & Alexandros Stamatakis
Introduction and overview of the course; Participants briefly introduce themselves within 2 minutes each
  10.15 - 12.00 Free tour of the CreteAcquarium
  12.00 - 13.30 Simon Berger
Unix/Windows command line basics and exercises
  13.30 - 15.00 Lunch
  15.00 - 16.30 Interpreting Molecular Phylogenetic Trees (I)
Aidan Budd & Brian Moore
Introducing applications of phylogenies; Introduction to phylogenetic terminology; Rooted/unrooted phylogenies; Branch lengths; A phylogenetic analysis work-flow
  16.30 - 17.00 Coffee
  17.00 - 18.30 Interpreting Molecular Phylogenetic Trees (II)
Aidan Budd & Brian Moore
  18.30 - 19.00 Break
  19.00 - 20.00 Evening Lecture - "The Tree of Life"
Martin Embley
  20:30 Dinner at hotel
     
Day 2
(Tuesday, 1 May 2012)
 
  09:00 - 10:00 Free Computing & Analysis practice
  10.00 - 11.30 Interpreting Molecular Phylogenetic Trees (III)
Aidan Budd & Brian Moore
  11.30 - 12.00 Coffee
  12.00 - 13.30 Interpreting Molecular Phylogenetic Trees (II)
Aidan Budd & Brian Moore
  13.30 - 15.00 Lunch
  15.00 - 16.30 Sequence Alignment (I)
Bill Pearson & Benjamin Redelings
Pairwise alignment; Searching sequence databases; Multiple sequence alignment (concepts, heuristics, softwares, "improvement by eye")
  16.30 - 17.00 Coffee
  17.00 - 18.30 Sequence Alignment (II)
Bill Pearson & Benjamin Redelings
  20.30 Dinner at Hotel
     
Day 3
(Wednesday, 2 May 2012)
 
  09:00 - 10:00 Free Computing & Analysis practice
  10.00 - 11.30 Sequence Alignment (III)
Bill Pearson & Benjamin Redelings
  11.30 - 12.00 Coffee
  12.00 - 13.30 Sequence Alignment (IV)
Bill Pearson & Benjamin Redelings
  13.30 - 15.00 Lunch and POSTER SESSION
  15.00 - 16.30 Sequence Alignment (V)
Bill Pearson & Benjamin Redelings
  16.30 - 17.00 Coffee
  17.00 - 18.30 Free Session
  20.30 Dinner at Hotel
     
Day 4
(Thursday, 3 May 2012)
 
  09:00 - 10:00 Free Computing & Analysis practice
  10.00 - 11.30 Phylogeny-reconstruction methods (I)
Maria Anisimova, Olivier Gascuel & John Huelsenbeck
Probabilistic models of character change/substitutions; Distance (minimum evolution, NJ, Fitch-Margoliash, etc.) and Parsimony methods; Likelihood and Bayesian methods; Tree search; Sources of error, both systematic and non-systematic
  11.30 - 12.00 Coffee
  12.00 - 13.30 Phylogeny-reconstruction methods (II)
Maria Anisimova, Olivier Gascuel & John Huelsenbeck
  13.30 - 15.00 Lunch and POSTER SESSION
  15.00 - 16.30 Phylogeny-reconstruction methods (III)
Maria Anisimova, Olivier Gascuel & John Huelsenbeck
  16.30 - 17.00 Coffee
  17.00 - 18.30 Phylogeny-reconstruction methods (IV)
Maria Anisimova, Olivier Gascuel & John Huelsenbeck
  18.30 - 19.00 Break
  19.00 - 20.00 Evening Lecture - "Evolutionary Genomics"
Antonis Rokas
  20.30 Dinner at Hotel
     
Day 5
(Friday, 4 May 2012)
 
  09:00 - 10:00 Free Computing & Analysis practice
  10.00 - 11.30 Phylogeny-reconstruction methods (V)
Maria Anisimova, Olivier Gascuel & John Huelsenbeck
  11.30 - 12.00 Coffee
  12.00 - 13.30 Phylogeny-reconstruction methods (VI)
Maria Anisimova, Olivier Gascuel & John Huelsenbeck
  13.30 - 15.00 Lunch
  15.00 - 16.30 Phylogeny-reconstruction methods (VII)
Maria Anisimova, Olivier Gascuel & John Huelsenbeck
  16.30 - 17.00 Coffee
  17.00 - 18.30 Phylogeny-reconstruction methods (VIII)
Maria Anisimova, Olivier Gascuel & John Huelsenbeck
  18.30 - 19.00 Break
  19.00 - 20.00 Evening Lecture - "Using phylogenetics to estimate species divergence times"
Jeff Thorne
  20.30 Dinner at Hotel
     
Day 6
(Saturday, 5 May 2012)
 
  09:00 - 10:00 Free Computing & Analysis practice
  10.00 - 11.30 Hypothesis testing in phylogenetics (I)
Nick Goldman & Ziheng Yang
Approaches (Likelihood/Bayesian); Tests of Substitution Models (Simple models [e.g. JC vs. HKY; PAM vs. WAG], Rate heterogeneity, Clocks, Selection/adaptation, others); Test of topologies (Bootstrapping [parametric and non-parametric], Comparisons of topologies [KH-test; SOWH-test]); Confidence sets/congruency of topologies (SH-test,Bayesian methods)
  11.30 - 12.00 Coffee
  12.00 - 13.30 Hypothesis testing in phylogenetics (II)
Nick Goldman & Ziheng Yang
  13.30 - 15.00 Lunch
  15.00 - 16.30 Hypothesis testing in phylogenetics (III)
Nick Goldman & Ziheng Yang
  16.30 - 17.00 Coffee
  17.00 - 18.30 Hypothesis testing in phylogenetics (IV)
Nick Goldman & Ziheng Yang
  18.30 - 19.00 Break
  19.00 - 20.00 Evening Lecture - "Natural Selection on the Mammalian Phylogeny"
Carolin Kosiol
  20.30 Dinner at Hotel
     
Day 7
(Sunday, 6 May 2012)
 
    Excursion and hike in the Rouvas gorge
     
Day 8
(Monday, 7 May 2012)
 
  09:00 - 10:00 Free Computing & Analysis practice
  10.00 - 11.30 Hypothesis testing in phylogenetics (V)
Nick Goldman & Ziheng Yang
  11.30 - 12.00 Coffee
  12.00 - 13.30 Hypothesis testing in phylogenetics (VI)
Nick Goldman & Ziheng Yang
  13.30 - 15.00 Lunch
  15.00 - 16.30 Hypothesis testing in phylogenetics (VII)
Nick Goldman & Ziheng Yang
  16.30 - 17.00 Coffee
  17.00 - 18.30 Using High Performance Parallel Computing for Phylogenetics
Alexandros Stamatakis
  20.30 Dinner at Hotel
     
Day 9
(Tuesday, 8 May 2012)
 
  09:00 - 10:00 Free Computing & Analysis practice
  10.00 - 11.30 Coalescent model and inference from population data (I)
Adam Leache & Bruce Rannala
  11.30 - 12.00 Coffee
  12.00 - 13.30 Coalescent model and inference from population data (II)
Adam Leache & Bruce Rannala
  13.30 - 15.00 Lunch
  15.00 - 16.30 Coalescent model and inference from population data (III)
Adam Leache & Bruce Rannala
  16.30 - 17.00 Coffee
  17.00 - 18.30 Coalescent model and inference from population data (IV)
Adam Leache & Bruce Rannala
  20.30 Dinner at Hotel
     
Day 10
(Wednesday, 9 May 2012)
 
  09:00 - 10:00 Free Computing & Analysis practice
  10.00 - 11.30 Coalescent model and inference from population data (V)
Adam Leache & Bruce Rannala
  11.30 - 12.00 Coffee
  12.00 - 13.30 Coalescent model and inference from population data (VI)
Adam Leache & Bruce Rannala
  13.30 - 15.00 Lunch
  15.00 - 16.30 Aidan Budd
Summary Exercise - Drawing together threads from earlier sessions Practical exercise working with data used in Phylogenetics in a court case: State of Louisiana v. Richard J. Schmidt.
  16.30 - 17.00 Coffee
  17.00 - 18.30 Aidan Budd
Summary Exercise - Drawing together threads from earlier sessions Final Questions, Feedback
  20.30 Dinner at Hotel
     
Day 11
(Thursday, 10 May 2012)
 
    Participants depart from Gouves

 

Teaching Assistants

 

Maria Anisimova

Detecting positive selection using codon models  
Computational Biochemistry Research Group, ETH Zurich, Switzerland 

 

Clemens Lakner

Bayesian inference of phylogenySchool of Computational Science
Florida State University, USA

 

Tim Massingham

Likelihood methods in phylogenetic analysis
EMBL - European Bioinformatics Institute, Hinxton, UK

  Aglaia (Cilia) Antoniou

Population genetics and phylogeography of animal species
Institute of Marine Biology and Genetics, HCMR, Greece

  Simon Berger

Heidelberg Institute for Theoretical Studies (HITS gGmbH), Heidelberg, Germany

  Pavlos Pavlidis Estimating number of species in samples of DNA sequences
Heidelberg Institute for Theoretical Studies, Germany
  Sarah Parks Likelihood methods in phylogenetic analysis
EMBL - European Bioinformatics Institute, UK

 

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