index.qmd

# Preface to {{< var ay >}} BM211 Workshop 5: Phylogenetic Trees {.unnumbered}

Welcome to the BM211 (Introduction to Microbiology) workshop on phylogenetic trees, for {{< var ay >}}.

This year is the first presentation of the workshop material in this format, and we would be very grateful to hear feedback [by email](mailto:{{< var admin.email >}}) or through the [GitHub repository Issues page]({{< var github.issues >}}).

## Overview

This workshop asks you to work through some computational exercises to gain some practice visualising and working with phylogenetic trees.

::: { .callout-note }
Phylogenetic trees are typically constructed _after_ sequence alignment has been performed. You learned about the fundamentals of (pairwise) sequence alignment in BM214 Workshop 2 -  [slides](https://classes.myplace.strath.ac.uk/mod/resource/view.php?id=1956504), [workshop](https://sipbs-compbiol.github.io/BM214-Workshop-2/). You may find it useful to refresh your memory about this topic.
:::

::: { .callout-warning title="Important Note" }
There is new material in this workshop that is not covered in lectures, and this material is examinable. Please take care to reach the text in the expandable callout boxes, as well as that for the workshop activities, to be sure you have understood the topic and obtain full value from the exercises.
:::

## Learning Objectives

By the end of this workshop, students will be able to:

- explain how a phylogenetic tree represents history and ancestry
- use `iToL` to visualise a variety of phylogenetic tree types
- describe and interpret the _topology_ of a tree
- generate a phylogenetic tree for a protein sequence and its homologues using UniProt, `MUSCLE`, and `iToL`
- explain the difference between a _gene tree_ and a _species tree_
- compare a gene tree with a species tree to interpret evolutionary history

## Assessment

The workshop is not formally assessed although, as noted above, all the material contained in the workshop is examinable. We have provided formative exercises to help you measure your progress.

::: { .callout-important }
There are 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 >}})
:::