The need for phylogenetic comparisons of molecular sequences has been increasing steadily with the explosive growth of genomic sequence data.  Estimation of species phylogenies and species divergence times, inference of population demographic processes and migration patterns, and delineation of species boundaries are central to our understanding of biodiversity and to interpreting genomic sequence data. 

Furthermore, molecular evolutionary analyses can provide important insights into the evolutionary process of sequences and genes: for example, detecting adaptive molecular evolution may be useful to disentangle viral infections and dynamics.  These processes can be analyzed via sophisticated statistical inference methods by means of efficient  algorithms that are implemented in a plethora of software packages.  However, empirical biologists often find it challenging to make effective use of those computational tools, partly due to the challenges in understanding their underlying statistical and computational principles.

Run biennially at the Genome Campus (and jointly with EMBL-EBI) this hands-on computational course aims to provide early-career stage researchers with the theoretical knowledge and practical skills to carry out molecular evolutionary analyses on sequence data.  The extensive programme comprises a mixture of lectures and computer practicals, and covers: data retrieval and assembly, alignment techniques, phylogeny reconstruction methods including maximum likelihood and Bayesian methods, hypothesis testing, and coalescent-based inference methods at the interface of phylogenetics and population genetics.  Besides acquiring the skills to properly deploy major software packages such as PhyML, RaXML, MrBayes, BEAST, BPP, etc., the course also focuses on statistical inference methods and algorithms. This will allow the participants to attain a thorough understanding of the underlying principles of the software they use.  

The course will also offer a unique opportunity for the participants to interact with some of the world-leading scientists and authors of famous software packages in evolutionary bioinformatics, including Nick Goldman, Tracy Heath, Brian Moore, Adam Leache, Bruce Rannala, Benjamin Redelings, Alexandros Stamatakis, Tanja Stadler, Jeff Thorne, and Ziheng Yang.

Target audience
The course is aimed primarily at biology and bioinformatics PhD students or postdocs in the early stages of their research career, and who already have some familiarity with phylogenetic methods (i.e., have already used some of the computer programs).  Programming experience is not required, although knowledge of R and experience in a scripting language such as python or perl will be very useful.  Candidates without prior experience with the Unix/Linux command line will be required to acquire these skills prior to the course. Training materials and exercises for improving Unix/Linux skills of participants will be provided before the course.

Feedback from the 2015 course

  • "Thank you for the excellent course!"
  • "Thank you for a fantastic and informative two weeks!!!"
  • "This course was very inspirational and i learned very many new skills here. I will use the software that was introduced during the course in my work. I found the all the Insturctors and TI-s very professional and easy to access. I also found the participants being from very different fields to be very enriching and i found many potential collaborators from the course."
  • "Thank you!!! Keep up the good work! The difference you make in our careers as early researchers cannot be stressed enough."
  • "Just keep offering the course, I think that what you are doing here is an incredibly valuable service to the community!"
  • "The instructors and teaching assistants were all a high point of the course. They were friendly, understanding and approachable"
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