Objective

This workshop is designed for graduate level students, postdoctoral fellows as well as professional researchers (both empiricists and theoreticians) in the fields of molecular evolution, molecular systematics, evolutionary biology, bioinformatics, genomics and statistics. Lectures on substitution models and molecular phylogeny given by local instructors will provide participants general background for attending the intensive lectures by the invited speaker, Prof. Zihen Yang.  Prof. Yang will introduce analysis methods for reconstructing phylogeny using likelihood-based approaches and Bayesian statistics, and methods for estimating the age of speciation as well as detecting adaptive evolution.  Hands-on software demonstration will also be included in the workshop.

Invited Speaker

Dr. Ziheng Yang
             Professor of Statistical Genetics at University College London

Schedule

12/21     Substitution Models (Chau-Ti Ting)                                                    

12/22     Phylogeny Reconstruction: Overview (Jer-Ming Hu)                          

              demo: phylip                                                                 

12/29     Chapter 4 Likelihood.pdf (Ziheng Yang)                                   

              demo: phylip & phyml

12/30     Chapter 5 Bayesian.pdf (Ziheng Yang)             

              demo: mrbayes

12/31     Molecular Clock and Estimation of Species Divergence Times

              Neutral and Adaptive Protein Evolution (Ziheng Yang)

01/01     demo: paml (mcmctree) & multidivtime (Ziheng Yang)

              demo: paml / codeml

Software

phylip: http://evolution.genetics.washington.edu/phylip.html

phyml: http://atgc.lirmm.fr/phyml/

mrbayes: http://mrbayes.csit.fsu.edu/

paml: http://abacus.gene.ucl.ac.uk/software/paml.html

multidivtime: http://statgen.ncsu.edu/thorne/multidivtime.html

Local Organizers

Chau-Ti Ting (ctting_at_ntu.edu.tw)

Jer-Ming Hu (jmhu_at_ntu.edu.tw)

Shun-Chern Tsaur (sctsaur_at_sinica.edu.tw)

SponsorNational Science Council

        Life Science College, National Taiwan University

        Research Center for Biodiversity, Academia Sinica