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summary.qmd
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summary.qmd
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# 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.
::: { .callout-tip title="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
:::
::: { .callout-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]({{< var myplace.bm211 >}}). You should complete these as part of the workshop.
- [Formative quiz 1]({{< var myplace.quiz1 >}})
- [Formative quiz 2]({{< var myplace.quiz2 >}})
- [Formative quiz 3]({{< var myplace.quiz3 >}})
- [Formative quiz 4]({{< var myplace.quiz4 >}})
:::
## That's All, Folks!
Thank you for taking part in this workshop. We hope you enjoyed it, and found it interesting.
::: { .callout-caution title="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](mailto:{{< var admin.email >}}) or through the [GitHub repository issues page]({{< var github.issues >}}).
:::