Day 1  |  Day 2 |  Day 3  |  Day 4 |  Day 5 |  Day 6 |  Day 7 |  Day 8  |  Day 9 |  Day 10

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Giorgos Kotoulas & Alexandros Stamatakis

a.m

Introduction and overview of the course; free tour of the CretAquarium;

participants briefly introduce themselves within 2 minutes each

a.m

Unix/Windows command line basics and exercises

Aidan Budd

topics: Introducing applications of phylogenies; Introduction to phylogenetic terminology, NEWICK/PHYLIP tree format; Rooted/unrooted phylogenies; Branch lengthsGene tree-species tree conflicts (gene duplication, horizontal transfer, lineage sorting); Phylogenetic networks

p.m

Interpreting molecular phylogenetic trees (I)

eve

Evening lecture 1:

Ken Wolfe: “Using phylogenetics to study gene and gene family evolution”

Day 2

(Tuesday May 4th 2010)

Aidan Budd

a.m

Interpreting molecular phylogenetic trees (II)

Bill Pearson & Javier Herrero

topics: Sequence databases (EMBL nucleotides; UniProt; others) and genome databases (Ensembl; UCSC genome browser; plants; bacteria; others); Databases of (or at least containing) alignments and/or trees (TreeBASE, Pfam, Pandit, TreeFam; others); Searching sequence databases (by keywords; by accession numbers; search software e.g. Blast; others);Pairwise alignment; Multiple sequence alignment (concepts, heuristics, softwares, “improvement by eye”); GBLOCKS (and others) to extract conserved blocks of alignments; Obtaining nucleotide alignments given protein alignment and associated nucleotide sequences – RevTrans (others); Struggling with formats — problems with getting your software of choice to accep your alignment of interest

p.m

Genomics resources and sequence alignment (I)

eve

Evening lecture 2:

Day 3

(Wednesday May 5th 2010)

Bill Pearson & Javier Herrero

a.m

Genomics resources and sequence alignment (II)

p.m

Participants can (no obligation) present research posters and talk about the posters with the lecturers/instructors

Day 4

(Thursday May 6th 2010)

Olivier Gascuel & John Huelsenbeck

opics: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, and approaches to address them:

Stochastic variation, Model mis-specification (base composition; substitution matrices; others), Long-branch attraction, Taxon-sampling;

others

a.m

Phylogeny-reconstruction methods (I)

p.m

Phylogeny-reconstruction methods (II)

eve

Evening lecture 3:

Aoife McLysaght: “Origins of New Genes”

Day 5

(Friday May 7th 2010)

Olivier Gascuel & John Huelsenbeck

a.m

Phylogeny-reconstruction methods (III)

p.m

Phylogeny-reconstruction methods (IV)

eve

Evening lecture 4:

Day 6

(Saturday May 8th 2010)

Mikkel Schierup & Rasmus Nielsen

topics:Fisher-Wright model and neutral coalescent; Population demography and subdivision; Ancestral polymorphism and lineage sorting

a.m

Coalescent model and inference from population data (I)

p.m

Coalescent model and inference from population data (II)

eve

Evening lecture 7:

Michail Averof: “Evolution of development”

Day 7

(Sunday May 9th 2010)

Excursion and hike in the Rouvas gorge

Day 8

(Monday May 10th 2010)

Nick Goldman & Ziheng Yang

topics: 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)

p.m

Hypothesis testing in phylogenetics (I)

eve

Evening lecture 6:

Antonis Rokas : “Experimental Molecular Evolution ”

Day 9

(Tuesday May 11th 2010)

Nick Goldman & Ziheng Yang

a.m

Hypothesis testing in phylogenetics(II)

p.m

Hypothesis testing in phylogenetics(III)

eve

Evening lecture 7:

Carolin Kosiol. : “Advances in codon models ”

Day 10

(Wednesday May 12th 2010)

Nick Goldman & Ziheng Yang

a.m

Hypothesis testing in phylogenetics(IV)

p.m

Q&A session - students can give oral presentations if they want to

Teaching Assistants