This course type is computational

Computational Molecular Evolution

08 - 19 May 2017Wellcome Genome Campus, Hinxton, UK
Deadlines (at 23:59 UTC):
  • Application Deadline Closed

  • Summary

    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”
  • Programme

    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.
  • Instructors / Speakers

    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

  • How to Apply

    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 / Bursaries

    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.