add basic instructions for iToL use

itol-visualisation-1.qmd

@@ -37,15 +37,21 @@ You can toggle between these two forms of _rectangular_ tree in `iTol` by changi
 
 Rotating a tree does not change its content or the relationships it describes. All four trees in @fig-four-rotated-trees show exactly the same information. These trees were generated by setting the `Rotation` value in the `iToL` control panel (@fig-itol-control-panel).
 
-::: { .callout-tip }
-Changing the _scaling_ of the tree (stretching or compressing it in any direction) also does not change the information presented. The trees in @fig-four-rotated trees were scaled horizontally by 50% using the `Advanced` tab of the `iToL` control panel (@fig-itol-control-panel-02).
+::: { .callout-tip collapse="true"}
+## Scaling and rotating trees in `iToL`
+
+To rotate your tree in `iToL`, use the `Rotation` setting in the `Mode Options` part of the `Basic` tab:
+
+![The `Basic` tab has a `Rotation` setting that you can use to rotate your tree through any angle](assets/images/itol-control-panel.png){#fig-itol-rotation width=80%}
+
+Changing the _scaling_ of the tree (stretching or compressing it in any direction) also does not change the information presented. The trees in @fig-four-rotated-trees were scaled horizontally by 50% using the `Advanced` tab of the `iToL` control panel (@fig-itol-control-panel-02).
 
 ![The advanced tab of the `iTol` control panel. Options in this menu allow you to change the way the tree is visualised.](assets/images/itol-control-panel-02.png){#fig-itol-control-panel-02 width=80%}
 
 :::
 
 
-::: {#fig-four-rotated-trees layout-ncol=2} 
+::: {#fig-four-rotated-trees layout-ncol=2 width=80%} 
 
 ![Default rotation, 0 degrees](assets/images/tree-newick-06.png){#fig-no-rotation width=80%}
 
@@ -75,6 +81,20 @@ Rotating the members of a clade around their common ancestor also does not affec
 The same cladogram, progressively rotating clades so that node order increases along the tree. The tree shows exactly the same information in each rotation - the _topology_ (branching order) of the tree remains unchanged.
 :::
 
+::: { .callout-tip collapse="true"}
+## Rotating a clade in `iToL`
+
+To rotate a clade in `iTol`, select the clade in the tree by clicking on its ancestral branch:
+
+![Select a clade in `iTol` by clicking on its ancestral branch](assets/images/itol-select clade.png){#fig-itol-select-clade width=80%}
+
+This will bring up a _context menu_ that includes the action to `Rotate children`. Clicking on the `Rotate children` action will rotate the two "child" branches of the clade around their common ancestor.
+
+![The clade _context menu_, showing the `Rotate children` action.](assets/images/itol-clade-context.png){#fig-itol-clade-context width=80%}
+
+![The result of rotating a clade](assets/images/itol-rotate-clade.png){#fig-itol-rotate-clade width=80%}
+:::
+
 ## Non-rectangular trees
 
 Phylogenetic trees do not need to be rectangular and, even if drawn using different forms, still present the same information as their rectangular counterparts.
@@ -92,6 +112,14 @@ The angle formed at each branching event doesn't need to be rectangular (at 90 d
 A rectangular and a slanted cladogram of the same phylogenetic tree, presenting identical evolutionary information.
 :::
 
+::: { .callout-tip collapse="true"}
+## Drawing a slanted cladogram in `iToL`
+
+To generate a slanted cladogram in `iTol`, select `Yes` for the `Slanted` option in the `Basic` tab:
+
+![The `Basic` tab has a `Rotation` setting that you can use to rotate your tree through any angle](assets/images/itol-control-panel-slanted.png){#fig-itol-slanted width=80%}
+:::
+
 ### Circular phylogram
 
 It is increasingly common, as datasets increase in size, to see _circular phylograms_ in publications. These place the root at the centre of a circle and show the branches as radii pointing away from the centre as genetic changes increase.
@@ -107,7 +135,15 @@ Rendering a tree in circular form does not change the information being presente
 A rectangular and a circular phylogram of the same phylogenetic tree, presenting identical evolutionary information.
 :::
 
-::: { .callout-tip title="Pros and cons of circular phylograms" }
+::: { .callout-tip collapse="true"}
+## Drawing a circular phylogram in `iToL`
+
+To generate a circular phylogram in `iTol`, select `Circular` mode in the `Basic` tab, and ensure that `Branch lengths` is set to `Use`:
+
+![Use the `Circular` mode to generate a circular tree in `iToL`](assets/images/itol-control-panel-circular.png){#fig-itol-circular width=80%}
+:::
+
+::: { .callout-caution title="Pros and cons of circular phylograms" collapse="true"}
 **Pros**
 
 - Circular trees are efficient with space 
@@ -117,4 +153,36 @@ A rectangular and a circular phylogram of the same phylogenetic tree, presenting
 
 - It can be difficult to read the labels on circular trees easily
 - Due to the way they are presented, especially for trees with lots of data, it can be difficult to see the branching order of nodes close to the root.
+:::
+
+### Unrooted trees
+
+All the trees you have seen so far have an implied _root_ - a single ancestral point from which all the sequences or species represented on the tree have descended. In terms of all like on Earth, we would call this root the [Last Universal Common Ancestor (LUCA)](https://astrobiology.nasa.gov/news/looking-for-luca-the-last-universal-common-ancestor/). For most trees we work with as scientists, the common ancestor would be much more recent than LUCA.
+
+::: { .callout-tip collapse="true"}
+## Rooted vs Unrooted Trees
+Some tree reconstruction methods, such as UPGMA or Neighbour-Joining (NJ) automatically produce _rooted_ trees, because of the way their algorithms work.
+
+Other, more accurate and precise, phylogenetic reconstruction methods such as Maximum Likelihood (ML) and Bayesian approaches produce _unrooted_ trees. These methods do not tell the user where the root of the tree is likely to be, so we often include an _outgroup_ - a species/sequence, or set of species/sequences that we already believe to be _ancestral to_ the part of the tree we're more focused on. This allows us to determine the most likely order of divergenece in that part of the tree.
+
+For example, if we wanted to produce a phylogenetic tree for primates, we would choose an _outgroup_ such as lagomorphs (rabbits, hares, etc.) oor colugos (Dermoptera), that diverged from an earlier common ancestor with primates (@Perelman2011-jg). 
+:::
+
+Unrooted trees, like that in @fig-unrooted-comparison, appear to extend out from a central point, **but that central point may or may not be the real root of the tree.** In @fig-unrooted-comparison, the rectangular tree implies that the root, i.e. the point at which the last common ancestor diverged into the ancestor of `M` and the ancestor of the remaining species, lies somewhere between M and the last common ancestor of `J` and `D`, **_not_** at the central junction in the tree. 
+
+::: {#fig-unrooted-comparison layout-ncol=2}
+
+![Rectangular phylogram](assets/images/tree-newick-17.png){#fig-rect-phyl2}
+
+![Unrooted phylogram](assets/images/tree-newick-18.png){#fig-unrooted}
+
+Rectangular and unrooted phylograms of the same phylogeny.
+:::
+
+::: { .callout-tip collapse="true"}
+## Drawing an unrooted tree in `iToL`
+
+To generate an unrooted tree in `iTol`, select `Unrooted` mode in the `Basic` tab:
+
+![Use the `Circular` mode to generate an unrooted tree in `iToL`](assets/images/itol-control-panel-unrooted.png){#fig-itol-unrooted width=80%}
 :::

references.bib

@@ -38,3 +38,40 @@ @ARTICLE{Yu2017-yq
   copyright = "http://onlinelibrary.wiley.com/termsAndConditions\#vor",
   language  = "en"
 }
+
+@ARTICLE{Perelman2011-jg,
+  title     = "A molecular phylogeny of living primates",
+  author    = "Perelman, Polina and Johnson, Warren E and Roos, Christian and
+               Seu{\'a}nez, Hector N and Horvath, Julie E and Moreira, Miguel A
+               M and Kessing, Bailey and Pontius, Joan and Roelke, Melody and
+               Rumpler, Yves and Schneider, Maria Paula C and Silva, Artur and
+               O'Brien, Stephen J and Pecon-Slattery, Jill",
+  abstract  = "Comparative genomic analyses of primates offer considerable
+               potential to define and understand the processes that mold,
+               shape, and transform the human genome. However, primate taxonomy
+               is both complex and controversial, with marginal unifying
+               consensus of the evolutionary hierarchy of extant primate
+               species. Here we provide new genomic sequence (~8 Mb) from 186
+               primates representing 61 (~90\%) of the described genera, and we
+               include outgroup species from Dermoptera, Scandentia, and
+               Lagomorpha. The resultant phylogeny is exceptionally robust and
+               illuminates events in primate evolution from ancient to recent,
+               clarifying numerous taxonomic controversies and providing new
+               data on human evolution. Ongoing speciation, reticulate
+               evolution, ancient relic lineages, unequal rates of evolution,
+               and disparate distributions of insertions/deletions among the
+               reconstructed primate lineages are uncovered. Our resolution of
+               the primate phylogeny provides an essential evolutionary
+               framework with far-reaching applications including: human
+               selection and adaptation, global emergence of zoonotic diseases,
+               mammalian comparative genomics, primate taxonomy, and
+               conservation of endangered species.",
+  journal   = "PLoS Genet.",
+  publisher = "Public Library of Science (PLoS)",
+  volume    =  7,
+  number    =  3,
+  pages     = "e1001342",
+  month     =  mar,
+  year      =  2011,
+  language  = "en"
+}