Programme
| Day 0 ( Sunday, 29 April 2012) |
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| Participants check in at the hotel in Gouves | ||
| Day 1 (Monday, 30 April 2012) |
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| 09.00 - 10.15 | Introductions Giorgos Kotoulas & Alexandros Stamatakis Introduction and overview of the course; Participants briefly introduce themselves within 2 minutes each |
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| 10.15 - 12.00 | Free tour of the CreteAcquarium | |
| 12.00 - 13.30 | Simon Berger Unix/Windows command line basics and exercises |
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| 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 |
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| 16.30 - 17.00 | Coffee | |
| 17.00 - 18.30 | Interpreting Molecular Phylogenetic Trees (II) Aidan Budd & Brian Moore |
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| 18.30 - 19.00 | Break | |
| 19.00 - 20.00 | Evening Lecture - "The Tree of Life" Martin Embley |
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| 20:30 | Dinner at hotel | |
| Day 2 (Tuesday, 1 May 2012) |
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| 09:00 - 10:00 | Free Computing & Analysis practice | |
| 10.00 - 11.30 | Interpreting Molecular Phylogenetic Trees (III) Aidan Budd & Brian Moore |
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| 11.30 - 12.00 | Coffee | |
| 12.00 - 13.30 | Interpreting Molecular Phylogenetic Trees (II) Aidan Budd & Brian Moore |
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| 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") |
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| 16.30 - 17.00 | Coffee | |
| 17.00 - 18.30 | Sequence Alignment (II) Bill Pearson & Benjamin Redelings |
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| 20.30 | Dinner at Hotel | |
| Day 3 (Wednesday, 2 May 2012) |
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| 09:00 - 10:00 | Free Computing & Analysis practice | |
| 10.00 - 11.30 | Sequence Alignment (III) Bill Pearson & Benjamin Redelings |
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| 11.30 - 12.00 | Coffee | |
| 12.00 - 13.30 | Sequence Alignment (IV) Bill Pearson & Benjamin Redelings |
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| 13.30 - 15.00 | Lunch and POSTER SESSION | |
| 15.00 - 16.30 | Sequence Alignment (V) Bill Pearson & Benjamin Redelings |
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| 16.30 - 17.00 | Coffee | |
| 17.00 - 18.30 | Free Session | |
| 20.30 | Dinner at Hotel | |
| Day 4 (Thursday, 3 May 2012) |
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| 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 |
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| 11.30 - 12.00 | Coffee | |
| 12.00 - 13.30 | Phylogeny-reconstruction methods (II) Maria Anisimova, Olivier Gascuel & John Huelsenbeck |
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| 13.30 - 15.00 | Lunch and POSTER SESSION | |
| 15.00 - 16.30 | Phylogeny-reconstruction methods (III) Maria Anisimova, Olivier Gascuel & John Huelsenbeck |
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| 16.30 - 17.00 | Coffee | |
| 17.00 - 18.30 | Phylogeny-reconstruction methods (IV) Maria Anisimova, Olivier Gascuel & John Huelsenbeck |
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| 18.30 - 19.00 | Break | |
| 19.00 - 20.00 | Evening Lecture - "Evolutionary Genomics" Antonis Rokas |
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| 20.30 | Dinner at Hotel | |
| Day 5 (Friday, 4 May 2012) |
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| 09:00 - 10:00 | Free Computing & Analysis practice | |
| 10.00 - 11.30 | Phylogeny-reconstruction methods (V) Maria Anisimova, Olivier Gascuel & John Huelsenbeck |
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| 11.30 - 12.00 | Coffee | |
| 12.00 - 13.30 | Phylogeny-reconstruction methods (VI) Maria Anisimova, Olivier Gascuel & John Huelsenbeck |
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| 13.30 - 15.00 | Lunch | |
| 15.00 - 16.30 | Phylogeny-reconstruction methods (VII) Maria Anisimova, Olivier Gascuel & John Huelsenbeck |
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| 16.30 - 17.00 | Coffee | |
| 17.00 - 18.30 | Phylogeny-reconstruction methods (VIII) Maria Anisimova, Olivier Gascuel & John Huelsenbeck |
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| 18.30 - 19.00 | Break | |
| 19.00 - 20.00 | Evening Lecture - "Using phylogenetics to estimate species divergence times" Jeff Thorne |
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| 20.30 | Dinner at Hotel | |
| Day 6 (Saturday, 5 May 2012) |
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| 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) |
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| 11.30 - 12.00 | Coffee | |
| 12.00 - 13.30 | Hypothesis testing in phylogenetics (II) Nick Goldman & Ziheng Yang |
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| 13.30 - 15.00 | Lunch | |
| 15.00 - 16.30 | Hypothesis testing in phylogenetics (III) Nick Goldman & Ziheng Yang |
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| 16.30 - 17.00 | Coffee | |
| 17.00 - 18.30 | Hypothesis testing in phylogenetics (IV) Nick Goldman & Ziheng Yang |
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| 18.30 - 19.00 | Break | |
| 19.00 - 20.00 | Evening Lecture - "Natural Selection on the Mammalian Phylogeny" Carolin Kosiol |
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| 20.30 | Dinner at Hotel | |
| Day 7 (Sunday, 6 May 2012) |
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| Excursion and hike in the Rouvas gorge | ||
| Day 8 (Monday, 7 May 2012) |
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| 09:00 - 10:00 | Free Computing & Analysis practice | |
| 10.00 - 11.30 | Hypothesis testing in phylogenetics (V) Nick Goldman & Ziheng Yang |
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| 11.30 - 12.00 | Coffee | |
| 12.00 - 13.30 | Hypothesis testing in phylogenetics (VI) Nick Goldman & Ziheng Yang |
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| 13.30 - 15.00 | Lunch | |
| 15.00 - 16.30 | Hypothesis testing in phylogenetics (VII) Nick Goldman & Ziheng Yang |
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| 16.30 - 17.00 | Coffee | |
| 17.00 - 18.30 | Using High Performance Parallel Computing for Phylogenetics Alexandros Stamatakis |
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| 20.30 | Dinner at Hotel | |
| Day 9 (Tuesday, 8 May 2012) |
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| 09:00 - 10:00 | Free Computing & Analysis practice | |
| 10.00 - 11.30 | Coalescent model and inference from population data (I) Adam Leache & Bruce Rannala |
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| 11.30 - 12.00 | Coffee | |
| 12.00 - 13.30 | Coalescent model and inference from population data (II) Adam Leache & Bruce Rannala |
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| 13.30 - 15.00 | Lunch | |
| 15.00 - 16.30 | Coalescent model and inference from population data (III) Adam Leache & Bruce Rannala |
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| 16.30 - 17.00 | Coffee | |
| 17.00 - 18.30 | Coalescent model and inference from population data (IV) Adam Leache & Bruce Rannala |
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| 20.30 | Dinner at Hotel | |
| Day 10 (Wednesday, 9 May 2012) |
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| 09:00 - 10:00 | Free Computing & Analysis practice | |
| 10.00 - 11.30 | Coalescent model and inference from population data (V) Adam Leache & Bruce Rannala |
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| 11.30 - 12.00 | Coffee | |
| 12.00 - 13.30 | Coalescent model and inference from population data (VI) Adam Leache & Bruce Rannala |
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| 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. |
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| 16.30 - 17.00 | Coffee | |
| 17.00 - 18.30 | Aidan Budd Summary Exercise - Drawing together threads from earlier sessions Final Questions, Feedback |
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| 20.30 | Dinner at Hotel | |
| Day 11 (Thursday, 10 May 2012) |
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| Participants depart from Gouves | ||
Teaching Assistants |
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Maria Anisimova |
Detecting positive selection using codon models |
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Clemens Lakner |
Bayesian inference of phylogenySchool of Computational Science |
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Tim Massingham |
Likelihood methods in phylogenetic analysis |
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| Aglaia (Cilia) Antoniou | Population genetics and phylogeography of animal species |
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| Simon Berger | Heidelberg Institute for Theoretical Studies (HITS gGmbH), Heidelberg, Germany |
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| Pavlos Pavlidis | Estimating number of species in samples of DNA sequences Heidelberg Institute for Theoretical Studies, Germany |
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| Sarah Parks | Likelihood methods in phylogenetic analysis EMBL - European Bioinformatics Institute, UK |