6 Summary
In this workshop you have learned how to build, visualise, and interpret phylogenetic trees. By using UniProt, MUSCLE, and iToL, you have been gaining experience with the same research-level tools that biologists and bioinformaticians use in their day-to-day work.
What you have learned
After working through the material, you should now be able to:
- upload a phylogenetic tree into
iToL - explain the meaning of branching events and branch lengths in a phylogenetic tree
- explain how a phylogenetic tree represents history and ancestry
- explain the concept of a clade in phylogenetics
- explain the difference between a phylogram and cladogram
- generate a variety of phylogenetic tree types using
iToL - describe and interpret the topology of a tree
- describe and interpret branch lengths of a tree
- explain how rotation of a tree, and clades within the tree, affects what the tree represents
- use UniProt to obtain annotation and functional information about a protein sequence
- use UniProt to identify and download homologues of a protein sequence
- generate a protein multiple sequence alignment using
MUSCLE - produce a Neighbour-Joining phylogenetic tree using
Simple Phylogeny - visualise a phylogenetic tree using
iToL - midpoint root a tree in
iToL - colour highlight clades of a tree in
iToL - explain the difference between a gene tree and a species tree
- compare a gene tree with a species tree to interpret evolutionary history
Important
If you have not done so already, please don’t forget to complete the four formative exercises in this workshop, and they can be found on the workshop MyPlace page. You should complete these as part of the workshop.
6.1 That’s All, Folks!
Thank you for taking part in this workshop. We hope you enjoyed it, and found it interesting.
Tell us about problems with the workshop, what you liked, or how you think it can be improved!
We would be very grateful to head feedback by email or through the GitHub repository issues page.