Introduction to Phylogenetics

Aligning sequences and building trees

The course aims to provide the basics of building and interpreting phylogenetic trees. It will provide lectures on the principle of phylogenetics and hands-on practice of using various freely-available programs used in phylogenetics studies.

Next session: Spring 2021

Instructors

Marielle Vigouroux
Jitender Cheema

Audience

Anyone with no or very little experience in phylogenetics.

Overview

The course is split over two half-days with the first half-day mostly covering alignments and the second half-day dedicated to building and analyzing phylogenetic trees. A surgery will be held on the afternoon of the second day where participants will have the opportunity to bring their own data.`

Schedule

Day 1

10:00	Start
11.30	Coffee break
13:00	End session 1

Day 2

10:00	Start
11:30	Coffee break
13:00	End session 2
14:00	Start of surgery
16:00	End of surgery

Learning outcomes

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

To be able to assess whether a phylogenetic analysis will help you to answer your biological question of interest
To have some understanding about what the major stages in a phylogenetic analysis are
To be able to run and edit a sequence alignment
To know how to build a simple tree
To be able to read and interpret a tree

Pre-requisites

No previous experience is needed.

Full course syllabus

Applications of phylogenetics
Major stages in phylogenetic analyses
Assembling a dataset
Multiple sequence alignment
Methods of phylogeny
Models of nucleotide sequence evolution
{'Aspect of phylogenies': 'topology, branches, nodes, root, confidence'}
Tree manipulation

Course materials

Course book