diff --git a/man/contents.rst b/man/contents.rst
index 7a10677..5d367c8 100644
--- a/man/contents.rst
+++ b/man/contents.rst
@@ -2,10 +2,9 @@ plot_phylo
 ==========
 
 .. toctree::
-   :maxdepth: 3
+   :maxdepth: 4
 
    index.md
-   pages/introduction.md
    pages/installation.md
    pages/quickstart.md
    pages/parameters.md
diff --git a/man/index.md b/man/index.md
index aa46c51..ea730a4 100644
--- a/man/index.md
+++ b/man/index.md
@@ -1,7 +1,18 @@
 # plot_phylo
+![Illustration](pages/examples/layered.png "Illustration")
+
+This module allows the user to plot a phylogenetic tree on an existing matplotlib axis.
+
+This means that:
+* Phylogenies can be incorporated into existing plots.
+* Annotations can be added using standard matplotlib functionality.
+* Plots can be output in png, pdf, svg or tiff formats.
+* Automatically generated and updated figures can include phylogenies
+
 1. [Installation](pages/installation.md)
 2. [Quick Start](pages/quickstart.md)
-3. [Incorporating Matplotlib Parameters](pages/matplotlib.md)
-4. [Parameters](pages/parameters.md)
+3. [Parameters](pages/parameters.md)
+4. [Incorporating Matplotlib Elements](pages/matplotlib.md)
 5. [Functions](pages/functions.md)
 6. [Detailed Example](pages/detailed.md)
+
diff --git a/man/pages/detailed.md b/man/pages/detailed.md
index 232bf42..9c5298d 100644
--- a/man/pages/detailed.md
+++ b/man/pages/detailed.md
@@ -1 +1,95 @@
-# Detailed Example
\ No newline at end of file
+# Detailed Example
+This detailed example shows how `plot_phylo` can be combined with matplotlib and basic Python to draw complex plots.
+
+```
+# Build the blank figure
+f = plt.figure(figsize=(15, 10))
+ax = plt.subplot(1, 1, 1)
+
+# Set the x and y axis limits
+ax.set_xlim(2, 122)
+ax.set_ylim(9, 21)
+ypos_val = 10
+
+# Define colours for specific nodes
+colours = {'Gorilla gorilla': '#e21c0c', 'Pan troglodytes': '#0c57e2', 'Saimiri boliviensis': '#338c3e',
+           'Chiropotes satanas': '#dc9d0c'}
+
+# Draw the left tree
+results_left = plot_phylo.plot_phylo("primates.nw",
+                                      ax, xpos=5, ypos=ypos_val, width=15,
+                                      show_axis=False, show_support=False,
+                                      font_size=16, col_dict=colours,
+                                      rev_align_tips=True)
+
+# Draw the right tree
+results_right = plot_phylo.plot_phylo("primates_mixed.nw",
+                                       ax, xpos=105, ypos=10, width=15,
+                                       show_axis=False, show_support=False,
+                                       reverse=True,
+                                       font_size=16, col_dict=colours,
+                                       rev_align_tips=True)
+
+# Using matplotlib and basic Python functionality on the returned dictionaries from hereforward
+
+# Connection between trees
+
+# Find the labels which differ between trees
+links = []
+for r1 in results_left:
+    # Find the index of each label in the tree
+    ind1 = results_left[r1]['index']
+    ind2 = results_right[r1]['index']
+    
+    # If they differ, store them
+    if ind1 != ind2:
+        links.append(r1)
+
+for link in links:
+    # Retrieve the positions of the non-matched labels
+    left_box = results_left[link]
+    right_box = results_right[link]
+    
+    # Get the position of the labels in each tree
+    left_x = left_box['xmax'] + 1
+    left_y = left_box['ymid']
+    
+    right_x = right_box['xmin'] - 1
+    right_y = right_box['ymid']
+
+    # Plot the points on the left tree
+    ax.scatter(left_x, left_y, color=colours[link])
+    
+    # Plot the points on the right tree
+    ax.scatter(right_x, right_y, color=colours[link])
+    
+    # Connect the two points
+    ax.plot([left_x, right_x], [left_y, right_y], color=colours[link])
+
+# Box highlighting great apes
+# Define which species are great apes
+great_apes = ['Gorilla gorilla', 'Pan troglodytes', 'Homo sapiens', 'Pongo abelii']
+ga_pos = []
+
+# Store the positions of the great ape labels
+for nam, box in results_left.items():
+    if nam in great_apes:
+        ga_pos.append(box['ymin'])
+        ga_pos.append(box['ymax'])
+
+# Draw the grey box. 15.5 is based on visually inspecting the axis.
+ax.fill_between([15.5, box['xmax']], min(ga_pos), max(ga_pos), color='lightgrey')
+
+# Additional labels
+# Add the Tree 1 and Tree 2 labels, using figure co-ordinates
+f.text(0.2, 0.85, 'Tree 1', ha='center', fontsize=16, fontweight='bold')
+f.text(0.8, 0.85, 'Tree 2', ha='center', fontsize=16, fontweight='bold')
+
+# Add the overall title
+f.suptitle("Primate Phylogeny", fontsize=24, y=0.92)
+
+# Save
+f.savefig("examples/layered.png", bbox_inches='tight')
+```
+
+![Detailed Example](./examples/layered.png "Detailed Example")
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diff --git a/man/pages/installation.md b/man/pages/installation.md
index 5e51873..f25cd4b 100644
--- a/man/pages/installation.md
+++ b/man/pages/installation.md
@@ -1,4 +1,4 @@
-## Installation
+# Installation
 
 **Requirements**
 
@@ -6,7 +6,6 @@
 * matplotlib >= 2.1.1
 * ete3 >= 3.1.0
 
-## Installation
 The module can be installed using pip
 
 `pip install plot_phylo`
diff --git a/man/pages/introduction.md b/man/pages/introduction.md
deleted file mode 100644
index 6cc9cd1..0000000
--- a/man/pages/introduction.md
+++ /dev/null
@@ -1,18 +0,0 @@
-# Introduction
-
-This module allows the user to plot a phylogenetic tree on an existing matplotlib axis.
-
-This means that:
-* Phylogenies can be incorporated into existing plots.
-* Annotations can be added using standard matplotlib functionality.
-* Plots can be output in png, pdf, svg or tiff formats.
-* Automatically generated and updated figures can include phylogenies
-
-1. [Installation](installation.md)
-2. [Quick Start](quickstart.md)
-3. [Incorporating Matplotlib Parameters](matplotlib.md)
-4. [Parameters](parameters.md)
-5. [Functions](functions.md)
-6. [Detailed Example](detailed.md)
-
-![Illustration](examples/layered.png "Illustration")
\ No newline at end of file
diff --git a/man/pages/matplotlib.md b/man/pages/matplotlib.md
index 4d70d59..1a0a434 100644
--- a/man/pages/matplotlib.md
+++ b/man/pages/matplotlib.md
@@ -1 +1,78 @@
-# Incorporating Matplotlib Parameters
\ No newline at end of file
+# Adding Matplotlib Elements to your Tree
+One of the main advantages of this module is that, as plots are generated using matplotlib and added to an active axis, other elements of matplotlib plots can be incorporated - the plot remains activate and can be edited.
+
+The plot_phylo function returns a dictionary where the keys are the tip labels and the values are the boundaries of the text boxes containing the tip labels, in axis units. 
+
+For example, the first few items in the list returned from the function call above are as follows:
+
+
+```
+{'Cercopithecus neglectus': {'index': 0,
+  'xmin': 9.656,
+  'xmax': 16.336,
+  'ymin': 9.882,
+  'ymax': 10.118,
+  'ymid': 10.0,
+  'xmid': 12.883},
+ 'Macaca mulatta': {'index': 1,
+  'xmin': 9.609,
+  'xmax': 14.2,
+  'ymin': 9.215,
+  'ymax': 9.452,
+  'ymid': 9.333,
+  'xmid': 12.101},
+ 'Colobus angolensis': {'index': 2,
+  'xmin': 9.649,
+  'xmax': 15.016,
+  'ymin': 8.548,
+  'ymax': 8.785,
+  'ymid': 8.667,
+  'xmid': 12.883},
+...
+```
+
+`xmin`, `xmid` and `xmax` are the positions of the left, centre and right of the tip label text on the x-axis.
+
+`ymin`, `ymid` and `ymax` are the positions of the bottom, centre and top of the tip label text on the y-axis.
+
+`ind` is the position of this label on the tree, reading from top to bottom, starting at 0.
+
+For example, for the first list item, Cercopithecus neglectus is the tip label. On the plot, this label spans positions 9.656 to 16.336 on the x-axis and 9.882 to 10.118 on the y axis. It is at position 0 in the tree.
+
+
+Providing these positions allows the user to add annotations etc. to the tip labels using matplotlib after drawing the plot.
+
+For example, here, the boundary box is of the first tip label is marked on the tree.
+
+```
+f = plt.figure(figsize=(8, 10))
+a = plt.subplot()
+
+# To use the text positions, the axis limits should be explicitly
+# specified before the plot is drawn
+
+plt.xlim(-2, 20)
+plt.ylim(-2, 11)
+
+# Draw the tree
+results = plot_phylo.plot_phylo("examples/primates.nw", a)
+
+# Retrieve the first result - for C. neglectus
+c_neg_results = results['Cercopithecus neglectus']
+
+# Plot these points on the axis
+# Bottom left
+plt.scatter(c_neg_results['xmin'], c_neg_results['ymin'], color='green', s=15)
+# Top left
+plt.scatter(c_neg_results['xmin'], c_neg_results['ymax'], color='red', s=15)
+# Bottom right
+plt.scatter(c_neg_results['xmax'], c_neg_results['ymin'], color='blue', s=15)
+# Top right
+plt.scatter(c_neg_results['xmax'], c_neg_results['ymax'], color='orange', s=15)
+
+# Save
+f.savefig("examples/basic_plot_box.png", bbox_inches='tight')
+
+```
+![Basic tree with box](./examples/basic_plot_box.png "Basic tree with box")
+
diff --git a/man/pages/parameters.md b/man/pages/parameters.md
index 1f49ec8..c912d95 100644
--- a/man/pages/parameters.md
+++ b/man/pages/parameters.md
@@ -1 +1,271 @@
-# Parameters
\ No newline at end of file
+# Parameters
+
+## Required
+### `tree`
+(`str`, Required)
+
+Either the path to a newick formatted tree or a string containing a newick formatted tree. 
+
+### `ax`
+(`matplotlib.axes._axes.Axes`, Required)
+
+An open matplotlib ax object where the tree will be plotted. Required.
+
+## Positioning the Plot
+Using the `xpos`, `ypos`, `height` and `width` parameters, the exact location of the tree within the axis can be specified.
+
+**`xpos`** defines the position of the most ancestral node in the tree on the x-axis, excluding the root. In the example tree, this is the split between the bottom three species (lemur, loris and galago) and the remaining primates.
+
+**`ypos`** defines the position of the bottom branch of the tree, on the y-axis. In the example tree, this is the branch leading to *Galago moholi*.
+
+**`width`** defines the width of the tree, excluding tip labels, in x-axis units. A tree with a `width` of 10 and and `xpos` of 5 will span from positions 5 to 15 on the x axis.
+
+**`height`** defines the height of the tree, excluding tip labels, in y-axis units. A tree with a `height` of 10 and and `ypos` of 5 will span from positions 5 to 15 on the y axis.
+
+For example:
+
+```
+# Draw the plot and set the axis limits
+f = plt.figure(figsize=(8, 10))
+ax = plt.subplot()
+ax.set_xlim(0, 60)
+ax.set_ylim(0, 20)
+
+# Set values for xpos, ypos, height and width
+xpos_val = 25
+ypos_val = 10
+height_val = 5
+width_val = 20
+
+# Run the plot_phylo function with these values
+results = plot_phylo.plot_phylo("examples/primates.nw", ax, xpos=xpos_val, ypos=ypos_val, height=height_val, width=width_val, show_axis=True, branch_lengths=False)
+
+# Annotate these points on the tree using matplotlib functions
+# Mark the bottom left corner
+ax.scatter(xpos_val, ypos_val, color='red', zorder=2)
+
+# Bottom right corner
+ax.scatter(xpos_val + width_val, ypos_val, color='blue', zorder=2)
+
+# Top left corner
+ax.scatter(xpos_val, ypos_val+height_val, color='green', zorder=2)
+
+# Top right corner
+ax.scatter(xpos_val+width_val, ypos_val+height_val, color='orange', zorder=2)
+
+# Draw a box around this region
+ax.plot([xpos_val,
+         xpos_val+width_val,
+         xpos_val+width_val,
+         xpos_val,
+         xpos_val],
+        [ypos_val,
+         ypos_val,
+         ypos_val+height_val,
+         ypos_val+height_val,
+         ypos_val], color='lightgrey', zorder=1)
+
+plt.savefig("examples/tree_pos.png", bbox_inches='tight')
+
+```
+![Position](./examples/tree_pos.png "Position")
+
+### `xpos`
+(`float`, Default 0)
+
+Desired position of the root of the tree on the x axis, in axis units. 
+
+### `ypos`
+(`float`, Default 0)
+
+Desired position of the bottom of the tree on the y axis, in axis units. 
+
+### `height`
+(`float`, Default 10)
+Desired height of the tree, in axis units. Regardless of the height of the axis, the tree with span from `ypos` to `ypos + height`.
+
+### `width`
+(`float`, Default 10)
+
+Desired width of the tree, in axis units. Default 10.
+
+## Visualisation Options
+### `show_axis`
+(`bool`, Default False)
+ 
+Show the axis lines and ticks on the output tree. 
+
+### `show_support`
+(`bool`, Default False)
+
+Display branch support on the internal nodes of the tree. 
+
+### `align_tips`
+(`bool`, Default False)
+
+If True, the tip labels will be horizontally aligned rather than positioned at the tips of the branches. By default, they are left-aligned for a standard tree and right-aligned for a mirrored tree (reverse=True)
+
+With `align_tips=True`
+```
+f = plt.figure(figsize=(8, 10))
+ax = plt.subplot()
+results = plot_phylo.plot_phylo("examples/primates.nw", ax, align_tips=True)
+plt.savefig("examples/align_tips.png", bbox_inches='tight')
+```
+
+![Aligned Tip Labels](./examples/align_tips.png "Aligned Tip Labels")
+
+### `rev_align_tips`
+(`bool`, Default False)
+
+If True the tip labels are right-aligned if reverse=False and left-aligned if reverse=True.
+
+With `rev_align_tips=True`
+
+```
+f = plt.figure(figsize=(8, 10))
+ax = plt.subplot()
+
+# For reverse aligned tip labels the axis limits need to be specified in advance
+ax.set_xlim(-1, 12)
+
+results = plot_phylo.plot_phylo("examples/primates.nw", ax, rev_align_tips=True)
+plt.savefig("examples/rev_align_tips.png", bbox_inches='tight')
+```
+![Reverse Aligned Tip Labels](./examples/rev_align_tips.png "Reverse Aligned Tip Labels")
+
+### `branch_lengths`
+(`bool`, Default True)
+
+If True, the branch lengths provided in the tree are used, otherwise all branches are fixed to the same length. The align tips function can be used in the same way regardless of whether branch lengths are used.
+
+With `branch_lengths=False`:
+
+```
+f = plt.figure(figsize=(8, 10))
+
+ax = plt.subplot()
+ax.set_xlim(-1, 20)
+# ylim is set explicitly before drawing the plot
+ax.set_ylim(-1, 10)
+
+results = plot_phylo.plot_phylo("examples/primates.nw", ax, branch_lengths=False)
+
+# Save the tree - matplotlib
+plt.savefig("examples/nobranchlengths.png", bbox_inches='tight')
+```
+![No branch lengths](./examples/nobranchlengths.png "No branch lengths")
+
+With `branch_lengths=False` and `align_tips=True`:
+
+```
+f = plt.figure(figsize=(8, 10))
+
+ax = plt.subplot()
+ax.set_xlim(-1, 20)
+# ylim is set explicitly before drawing the plot
+ax.set_ylim(-1, 10)
+
+results = plot_phylo.plot_phylo("examples/primates.nw", ax, branch_lengths=False, align_tips=True)
+
+# Save the tree - matplotlib
+plt.savefig("examples/nobranchlengths_ali.png", bbox_inches='tight')
+```
+![No branch lengths aligned](./examples/nobranchlengths_ali.png "No branch lengths aligned")
+
+### `scale_bar`
+(`bool`, Default True)
+
+If True and branch_lengths is True, draw a scale bar.
+ 
+### `scale_bar_width`
+(`float`, Default None)
+
+Width of scale bar in axis units. If not specified, the scale bar will be 1/4 of the width of the tree.
+
+### `reverse`
+(`bool`, Default False)
+*
+If True, mirror the tree on the y-axis, showing the root on the right-hand side.
+
+With `reverse=True`:
+
+```
+f = plt.figure(figsize=(8, 10))
+ax = plt.subplot()
+results = plot_phylo.plot_phylo("examples/primates.nw", ax, reverse=True)
+plt.savefig("examples/reversed.png", bbox_inches='tight')
+```
+
+![Mirrored Tree](./examples/reversed.png "Mirrored Tree")
+
+### `outgroup`
+(`str`, Default None)
+
+Specifies a leaf to set as the outgroup, must be identical to the name in the tree file.
+
+### `col_dict`
+(`dict`, Default {})
+
+User provided dictionary with tip labels as keys and colours (in any [format accepted by matplotlib](https://matplotlib.org/stable/users/explain/colors/colors.html) as values. If this is not specified all labels will be black, if only some labels are specified all others will be black.
+
+With `col_dict={'Macaca mulatta': 'orange, 'Gorilla gorilla': 'blue'}`:
+
+```
+f = plt.figure(figsize=(8, 10))
+ax = plt.subplot()
+results = plot_phylo.plot_phylo("examples/primates.nw", ax, col_dict={'Macaca mulatta': 'orange', 'Gorilla gorilla': 'blue'})
+plt.savefig("examples/colours.png", bbox_inches='tight')
+```
+
+![Coloured tip labels](./examples/colours.png "Coloured tip labels")
+
+
+### `label_dict`
+(`dict`, Default {})
+
+User provided dictionary with current tip labels as keys and desired
+tip labels as values. If this is not specified all labels will be as specified in the newick, if some labels are specified all others will match the newick.
+
+With `label_dict={'Macaca mulatta': 'Rhesus macaque, 'Homo sapiens': 'human'}`: 
+
+```
+f = plt.figure(figsize=(8, 10))
+ax = plt.subplot()
+results = plot_phylo.plot_phylo("examples/primates.nw", ax, label_dict={'Macaca mulatta': 'Rhesus macaque', 'Homo sapiens': 'human'},
+col_dict={'Macaca mulatta': 'orange', 'Homo sapiens': 'blue'})
+plt.savefig("examples/labels.png", bbox_inches='tight')
+```
+
+![Renamed tips](./examples/labels.png "Coloured tip labels")
+
+
+### `font_size`
+(`int`, Default 10)
+
+Font size for tip labels. Branch support and scale bar labels will be two sizes smaller.
+ 
+### `line_col`
+(`str` or `tuple`, Default 'black')
+
+Line colour, in any [format accepted by matplotlib](https://matplotlib.org/stable/users/explain/colors/colors.html).
+
+### `line_width`
+(`float`, Default 2)
+
+Line width.
+	
+### `bold`
+(`list`, Default `[]`)
+
+A list of sequence names to show in bold. If sequences are renamed using `label_dict`, provide the original names.
+
+With `bold=['Homo sapiens']`:
+```
+f = plt.figure(figsize=(8, 10))
+ax = plt.subplot()
+results = plot_phylo.plot_phylo("%s/examples/primates.nw" % path, ax, bold=['Homo sapiens'])
+plt.savefig("examples/bold.png", bbox_inches='tight')
+```
+  
+![Bold](./examples/bold.png "Bold")
diff --git a/man/pages/quickstart.md b/man/pages/quickstart.md
index 1d2e852..74860de 100644
--- a/man/pages/quickstart.md
+++ b/man/pages/quickstart.md
@@ -1 +1,23 @@
-# Quick Start
\ No newline at end of file
+# Quick Start
+
+To draw a phylogeny under the default settings onto a blank figure.
+
+```
+import matplotlib.pyplot as plt
+import plot_phylo
+
+# Create an empty plot, 8in (width) by 10in (height) - matplotlib
+f = plt.figure(figsize=(8, 10))
+
+# Add an axis - matplotlib
+ax = plt.subplot()
+
+# Plot the tree on this axis, using the default settings - plot_phylo
+results = plot_phylo.plot_phylo("examples/primates.nw", ax)
+
+# Save the tree - matplotlib
+plt.savefig("examples/basic_plot.png", bbox_inches='tight')
+```
+
+The output of this function is:
+![Basic Tree](./examples/basic_plot.png "Basic Tree")
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