Merge pull request #101 from SPAAM-community/figtree-typofixes

Fix confusing formatting figtree

Author: jfy133

phylogenomics.qmd

@@ -51,7 +51,7 @@ If so, it means that the tree is oriented in time, such that we can define which
 We call such tree a _rooted tree_.
 Note that time-trees are rooted by definition (but the opposite is not true).
 Substitution trees are in principle unrooted, as these contain information about the genetic distance between nodes, but not about the relative age of nodes.
-Unrooted trees are best represented in a star-shaped manner (although visualization softwares such as `FigTree` present all trees as if they were rooted, by default).
+Unrooted trees are best represented in a star-shaped manner (although visualization softwares such as `figtree` present all trees as if they were rooted, by default).
 
 
 ![Rooted _versus_ unrooted tree.](assets/images/chapters/phylogenomics/rooted_tree.png){#fig-phylogenomics-rooted_tree}
@@ -235,7 +235,7 @@ This includes:
 _note:_ a "substitution" is a type of mutation in which a nucleotide is replaced by another.
 :::
 
-Since the tree is not easily visualised in `MEGA`, we will export it in newick format (a standard text format for trees) and open it in `FigTree`.
+Since the tree is not easily visualised in `MEGA`, we will export it in newick format (a standard text format for trees) and open it in `figtree`.
 This tool has a better graphical interface for visualizing and manipulating trees.
 
 To do that, click on `File`, then `Export current tree (Newick)` and click on `Branch Lengths` to include those in the newick annotation.
@@ -245,7 +245,7 @@ You can then close the text editor and tree explorer windows (no need to save th
 
 ![Exporting the tree in newick format.](assets/images/chapters/phylogenomics/10.png){#fig-phylogenomics-10}
 
-As said above, we will explore oun NJ tree in `FigTree`.
+As said above, we will explore oun NJ tree in `figtree`.
 Open the software (if you use the same terminal window as the one in which you ran MEGA, you might have to press ```enter``` first).
 
 ```bash
@@ -256,7 +256,7 @@ Then, open the NJ tree by clicking on `File -> Open` and selecting the file with
 
 ![Opening a tree in FigTree](assets/images/chapters/phylogenomics/11.png){#fig-phylogenomics-11}
 
-Note that even though a root is displayed by default in `FigTree`, NJ trees are actually _unrooted_.
+Note that even though a root is displayed by default in `figtree`, NJ trees are actually _unrooted_.
 We know that _Yersinia pseudotuberculosis_ (labelled here as _Y. pseudotuberculosis_) is an outgroup to _Yersinia pestis_.
 You can reroot the tree by selecting _Y.pseudotuberculosis_ and pressing `Reroot`.
 
@@ -357,7 +357,7 @@ Once the analysis has been completed, you can open the tree using `FigTree`(RAxM
 
 The tree estimated using this model is a substitution tree (branch lengths represent genetic distances in substitutions/site).
 As for the NJ tree, it is not oriented in time: this is an unrooted tree (displayed with a random root in Figtree).
-You can reroot the tree in `FigTree` using _Y. pseudotuberculosis_ as an outgroup, as previously.
+You can reroot the tree in `figtree` using _Y. pseudotuberculosis_ as an outgroup, as previously.
 
 ::: {.callout-tip title="Question" appearance="simple"}
 Can you confirm the position of our genomes of interest (KZL002, GZL002, CHC004 and VLI092)?