Introduction to Phylogenetics (IN-PERSON)

Prerequisites

This course will teach you how to use molecular data to construct and interpret phylogenies. We will start by introducing basic concepts in phylogenetic analysis, what trees represent and how to interpret them. We will then cover how to produce a multiple sequence alignment from DNA and protein sequences, and the pros and cons of different alignment algorithms. You will then learn about different methods of phylogenetic inference, with a particular focus on maximum likelihood and how to assess confidence in your tree using bootstrap resampling. Finally, we will introduce how Bayesian methods can help to estimate the uncertainty in the inferred tree parameters as well as incorporate information for more advanced/bespoke phylogenetic analysis.

If you do not have a University of Cambridge Raven account please book or register your interest here.

• ♿ The training room is located on the first floor and there is currently no wheelchair or level access.
• Our courses are only free for registered University of Cambridge students. All other participants will be charged according to our charging policy.
• Attendance will be taken on all courses and a charge is applied for non-attendance, including for University of Cambridge students. After you have booked a place, if you are unable to attend any of the live sessions, please email the Bioinfo Team.
• Further details regarding eligibility criteria are available here.
• Guidance on visiting Cambridge and finding accommodation is available here.

• This course is aimed at researchers with no prior experience in phylogenetic analysis who would like an introduction to the foundations of building phylogenies from relatively small sequences (viral genomes and/or targeted regions of eukaryotic genomes).
  • Note that we will not cover specific topics in phylogenomics (whole-genome phylogenies) or bacterial genomics.
• Graduate students, Postdocs and other Research Staff from the University of Cambridge, Affiliated Institutions and other external institutions or individuals.

• Familiarity with the Unix command line is essential. We provide a self-assessment quiz, which you can use to check your suitability for this course. Otherwise, please make sure to attend our Unix course ahead of this course.
• Familiarity with basic concepts in evolution (descent from a common ancestor, sequence divergence due to mutations, natural selection).
• Basic experience of examining DNA/protein sequence data.

Bioinformatics, Data handling, Data mining, Data visualisation, Phylogenetics

After this course you should be able to:

• Describe the process of constructing molecular phylogenetic trees and how to interpret them.
• Reconstruct trees from sequence data, choosing an appropriate set of tools and models.
• Have an overview of the software available for phylogenetic tree reconstruction.
• Recognise the advantages and disadvantages of different methods and make an informed choice on which to choose.
• Interpret the phylogenetic inference results with regards to evolutionary information, robustness and potential inaccuracies.

During this course you will learn about:

• Producing a multiple sequence alignment from related sequences and identify quality issues with the resulting alignment.
• Infer phylogenetic trees using maximum likelihood methods, including how to choose suitable substitution models for your data.
• Assess the robustness of your tree using the bootstrap method, and recognise its limitations.
• Become familiar with standard file formats to represent sequences (FASTA) and trees (Newick) as well as tools to manipulate and visualise them.
• Apply Bayesian methods for divergence time estimation.

Presentations, demonstrations and practicals

• Free for registered University of Cambridge students
• £ 60/day for all University of Cambridge staff, including postdocs, temporary visitors (students and researchers) and participants from Affiliated Institutions. Please note that these charges are recovered by us at the Institutional level
• It remains the participant's responsibility to acquire prior approval from the relevant group leader, line manager or budget holder to attend the course. It is requested that people booking only do so with the agreement of the relevant party as costs will be charged back to your Lab Head or Group Supervisor.
• £ 60/day for all other academic participants from external Institutions and charitable organizations. These charges must be paid at registration
• £ 120/day for all Industry participants. These charges must be paid at registration
• Further details regarding the charging policy are available here

1

Once a year

• Introduction to working with UNIX and bash (IN-PERSON)