GenEpi-BioTrain - Virtual training 07 - Phylogenetics and alignments

Topic outline

• Phylogenetics and alignments (GenEpi-BioTrain - Virtual training 7)

  Phylogenetics and alignments (GenEpi-BioTrain - Virtual training 7)

  ℹ️ Please Note

  You are welcome to explore the available resources and video recordings. Please note that the resources in this course come from the Virtual Training 07  held in March 2024, and certificates are only issued to participants who attended the live webinar sessions.

  
  Welcome to this virtual training space on EVA.

  Below you will see the two online sessions and their support materials.

  In anticipation for the live sessions, we encourage participants to:

  1. Explore the materials available; 

  2. Install the software indicated below;

  3. Suggest topics of interest for future virtual trainings.

  
  

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• Aim and objectives

  Aim and objectives

  The aim of this virtual training is to introduce participants to theoretical and practical aspects of alignments and phylogenetics. Participants will gain a basic understanding of what a phylogeny is, and how it can be generated and assessed for quality and trustworthiness.
  

  Upon completion of this workshop, participants will be able to:

  • Describe what phylogeny is;
  • Generate phylogenies using state-of-the-art tools for alignments and phylogenetic inference; 
  • Evaluate the quality and trustworthiness of a phylogeny.

  
  
• Delivery

  Delivery

  Format

  This virtual training takes place over two sessions that will be held on 19 and 20 March 2024, 12:30-16:00 (CET). 

  
  

  Outline

  Session 1: 

  Part 1: Lecture on evolution, phylogeny and alignment. 

  Part 2: Exercise on alignments.

  Session 2: 
  

  Part 1: Lecture on phylogenetic methods.

  Part 2: Exercise on phylogenetic analysis.

  
  

  Prerequisites

  For the general lectures there are no prerequisites. 

  The minimal prerequisites for participants to meet the learning objectives of the workshop are: 

  • Have the software mentioned below installed.

  
  

  For meeting the full learning objectives, you should be familiar with using a command-line terminal: 

  • Be familiar with running bioinformatic command line tools;
  • Have conda, miniconda or equivalent installed.

  Alternative learning materials will be offered during this session so that all participants can take part in the following activities and discussions.
• Software requirements

  Software requirements

  For the general lectures there are no software requirements.
  

  The minimal prerequisites for participants to meet the learning objectives of the practical part are installation of the following software:

  • Figtree (http://tree.bio.ed.ac.uk/software/figtree/)
  • Jalview (https://www.jalview.org)
  • MEGA ≥v10 (https://www.megasoftware.net)
  • A Web browser (in order to use Microreact and iTol and to visualize a .png image)

  
  To have the full experience of the practical part, you should have a terminal with one or more (Conda) environment(s) containing the following software:

  
  

  Session 1

  •  "python>=3.7"
  •  "blast>=2"
  •  "mafft>=7"
  •  mlst=2
  •  muscle=5
  •  "snippy>=4.6"

  
  Session 2:
  

  • "python>=3.7"
    
  • ete3=3.1
    
  • iqtree=2.2
    
  • fasttree=2.1
    
  • "gubbins>=2"
    
  • pandas=2

  (if using Conda, use channels Conda-forge and bioconda)

  Data used in the webinar exercises:

  All data for the webinar exercises is available on GitHub: https://github.com/ssi-dk/GenEpi-BioTrain_Virtual_Training_7

  We recommend all participants to clone the repository to their local machines and install the conda environments as described on the landing page. Together with installing the above standalone software, this will allow you to perform all the exercises.

  Note: The repository is subject to continuous updates, so we recommend pulling the latest changes just before starting the exercise sessions. 
• Session 1 (19 March)

  Session 1 (19 March)

  Part 1 (Theory): Evolution, phylogeny and alignment

  Topics

  • Evolution basics, mutations
    
  • The purpose of and uses for sequence alignment
    
  • The basics of sequence alignment algoritms; scoring schemes, substitution matrices and gap penalties
    
  • Global alignment, Multiple Sequence Alignment (MSA) and local alignment
    
  • Methods for sequence alignment 

   Part 2 (Practical): Alignments

  Tasks

  • Generate a simple pairwise sequence alignment using the Needleman-Wunsch algorithm
    
  • Generate a multiple sequence alignment using MAFFT and MUSCLE
  • Use BLAST on command line to identify shared regions between two sequence collections and align those regions
    
  • Run a core genome SNP analysis using snippy 

  
  

  • FolderPresentations
  • FolderExercise

• Session 2 (20 March)

  Session 2 (20 March)

  Part 1 (Theory): Phylogenetic methods

  Topics

  • What is a tree? 
  • How to read a phylogenetic tree 
  • Tree rooting (midpoint, outgroup) 
  • Tree storing formats (Newick, NeXus, XML) 
  • Maximum parsimony 
  • Substitution models 
  • Distance-based (NJ, UPGMA, Least squares) 
  • Probabilistic methods: (ML, Bayesian) 
  • Advanced phylogenetic analyses: 
  • Timescaled trees 
  • Ancestral state reconstruction 
  • Mapping natural selection 
  • Software: DistBased (MEGA, PAUP, etc.), ML (PhyML, RAxML, IQ-TREE), Bayesian (BEAST, MrBayes, etc.), FastTree 

   Part 2 (Practical): Phylogenetic analysis

  Tasks

  • Construct phylogeny on alignments from Session 1/Part 2 using different methods using the software MEGA, IQ-TREE and FastTree 
  • Handle recombination in core-genome SNP alignments using Gubbins 
  • Visualize the trees in Microreact, iTOL (web), and ETE3 (Python) 

  • FolderPresentations
  • FolderExercise

• Contacts

  Contacts

  For any questions regarding the this virtual training, please use the discussion forum.

  If you have questions about the GenEpi-BioTrain programme, please address ECDC.Microbiology@ecdc.europa.eu.

  If you have questions regarding other training initiatives please contact: Courses@ecdc.europa.eu.

  If you have technical issues please contact ECDC Front Office FrontOffice@ecdc.europa.eu.