Module 3.2 - Getting started with phylogenies (outline)
Theme 3: Genome analysis and sharing
Getting started with phylogenies
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Time |
Activity description |
ILOs |
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9.00-9.45 |
Lecture: “Evolution and phylogenies” |
· Provide examples of how evolution acts on genomes · Explain how we can reconstruct evolutionary relationships from genes and genomes |
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10.00-12.00 |
Practical: “Sequence handling and alignment” |
· Align genomic sequences with different aligner tools · Understand the impact of changing parameters · Understand that the choice of software can have a major impact on the results · Independently gather and align sequences with appropriate methods · Type strains with MLST |
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13.00-14.00 |
Lecture: “Phylogenetic analysis” |
· Understand basic concepts for phylogenetic reconstruction · Appreciate that a wide range of tools are available for phylogenetic inference, and have an idea about how to make a software choice · Summarise some of the models used in phylogenetic reconstruction · Describe major parameters used to evaluate the quality and trustworthiness of a phylogeny |
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14.30-16.30 |
Practical: “Phylogenetic analysis” |
· Run different phylogenetic tools and models on a sequence alignment · Evaluate and compare phylogenetic results |
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Details
Phylogenies play an important role in genome-based pathogen surveillance, both for classification of new isolates and outbreak analysis. In this module, the participants will gain a basic understanding of what a phylogeny is, and how they can be generated. The participants will also get familiar with common parameters used to evaluate the quality and trustworthiness of a phylogeny.