Computational Molecular Evolution

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”

The programme will include lecture and practical computer-based sessions
covering the following topics:

• Data retrieval and assembly
• Next Generation Sequencing (NGS) technologies*
• Alignment techniques
• Phylogeny reconstruction
• Statistical tests of phylogenetic hypotheses
• Detection of molecular adaptation
• Molecular clock dating integrating fossil and morphological evidence
• Species tree estimation and species delimitation under the multispecies coalescent model
• Parallel computing

*Please note: The course focuses on NGS
analyses for molecular evolution and does not include tutorials on the
traditional DNA-seq or RNA-seq data processing (QC, read mapping, SNP
calling, expression analysis, assembly etc).

Additional sessions
There will also be the opportunity for a
limited number of participants
with programming experience in
bioinformatics to participate in 2–3
‘hands-on’ coding sessions led by
the course instructors.

Learning outcomes
The overall aim is to enable participants to critically review, assess
and apply quantitative computational methods for evolutionary data
analyses.

By the end of the course participants should be able to:

• Interpret evolutionary trees and recognise / discuss the power of molecular phylogenies for understanding real-world biological questions, relating to evolutionary history, current-day biodiversity and future diversification of living organisms
• Browse, query and extract genome sequence from public databases, and create multiple sequence alignments.
• Employ appropriate bioinformatics skills that also allow for the analysis of large genome-scale datasets, including command line use of specialist software, simple scripting, compiling programs and submitting jobs on multi-core servers and compute clusters.
• Select and apply appropriate commonly used phylogenetic software packages (such as PhyML, RAxML, PAML, MrBayes, BEAST) to infer phylogenetic trees, estimate divergence times, and test phylogenetic hypotheses.
• Understand and explain the underlying principles of major phylogenetic methods such as distance matrix-based, maximum likelihood, and Bayesian methods, including the MCMC method.
• Understand and explain the use of Markov models of nucleotide, amino acid and codon substitution, hypothesis testing using the likelihood ratio test, coalescent and multispecies coalescent models in species tree estimation and species delimitation.
• Apply likelihood ratio tests to infer the existence and location of molecular adaptation affecting protein-coding genes.

Lead instructors
Nick Goldman European Bioinformatics Institute, Hinxton, UK
Ziheng Yang University College London, UK
Alexandros Stamatakis Heidelberg Institute for Theoretical Studies, Germany
Aglaia (Cilia) Antoniou Hellenic Centre for Marine Research, Greece

Prerequisites
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.

Cost
The
course is subsidised by the Wellcome Genome Campus Advanced Courses
and Scientific Conferences Programme. This is a residential
course and
there is a fee of £1660 towards board and lodging for
non-commercial applicants. Please contact us for the commercial fee.

Additional limited bursaries are available (up to 50%
of the course fee)
and are awarded on merit. Please see the “Bursaries”
tab for details.

Applications
Applications for this course can be completed online. If you have any
problems with the online application process, please contact us.

Please note: Applications
must be supported by a
recommendation from a scientific or clinical sponsor (e.g. supervisor or
head of department). A request for a supporting
statement will be sent
to your nominated sponsor automatically during
the application process.
Applicants must ensure that their sponsor
provides this supporting
statement by the application deadline. Applications without a supporting
statement cannot be considered.

Deadlines
Deadline for Applications: Closed

Travel visas
Please contact the
event organiser if you require a letter to support a
travel visa
application. Note that letters will be provided to confirmed
attendees.

Non-European Economic Area or Swiss nationals may be required to have a
visa to enter the UK.
Early application is strongly advised, as this process can take 6-8 weeks
or longer.

Please visit the following websites for further information:
UK Border Agency website and information for general visitors and business
visitors.

Cost
The
course is subsidised by the Wellcome Genome Campus Advanced Courses
and
Scientific Conferences Programme. This is a residential
course and
there is a fee of £1660 towards board and lodging for
non-commercial applicants. Please contact us for the commercial fee.

Bursaries
Advanced Courses are subsidised for non-commercial applicants from
anywhere in the world. Additional, limited bursaries are
available (up
to 50% of the course fee) and are awarded on merit. If you would like to
apply for a
bursary, please complete the bursary section of the online
application
form.

Please note that both the applicant
and sponsor are required to provide
a justification for the
bursary as part of the application.

Bursary terms and conditions

UK Courses (held at the Wellcome Genome Campus, Hinxton,
Cambridge)
A
limited number of bursaries are available for each course. These are
awarded by the selection committee according to merit. The bursary
covers a maximum of 50% of the course fee, though in exceptional
circumstances an application for the total course fee may be considered.
Where there are many bursary applications, the selection committee may
issue smaller amounts. We cannot assist with travel costs to attend UK
courses.

Overseas Courses (held outside of the UK)
A
limited number of bursaries are available for each course. These are
awarded on merit to cover travel, accommodation and sustenance. The
maximum award for travel (economy class) will be £750.

Bursaries can be applied for as part of the course application form.
Applicants
will be notified of a bursary award along with their place on
the
course, usually within one month of the application deadline. The
decision of the selection committee is
final.