Phyloview Tutorial


Palidwor, G., E.G. Reynaud, and M.A. Andrade-Navarro. 2006. Taxonomic colouring of 
phylogenetic trees of protein sequences. BMC Bioinformatics. 7, 79.


Introduction
PhyloView is a program designed to provide phylogenetic colouring of 
protein derived phylogenetic trees. It runs in a web browser.


Requirements

Internet Explorer v6.0 (or higher)
Adobe SVG Viewer



Input File Format
Phyloview takes data in Newick tree format (described here). This is a text format which 
represents trees as a series of nested brackets. It is generated from multiple sequence 
alignments by programs like ClustalX.




Tutorial

Open the PhyloView tool (link will open in new window).
Right click on the following link and select "Save As" in an appropriate 
directory. if2_fasta.phr. This is a Newick tree format file of IF2G related
proteins.
Click on the "Browse" button in the left hand PhyloView Pane and select
the previously downloaded if2_fasta.phr file, then click on the 
"Upload File" button. 
The left hand pane should now reload, and an expandable taxonomy tree will then 
appear. This tree contains the full taxonomy tree of all of the proteins in the 
uploaded tree. The tree may be traversed by clicking on triangles to expand/collapse. 
If the boxes in this pane are clicked, a colour may be selected for the specified 
taxonomic node.
After selecting the colours as above, click on the "Render Tree" button
to render the tree. The tree should appear in the right hand window, coloured as 
specified in the taxonomic colour selection tree. Clicking on the leaf nodes will
open a new browser window showing the appropriate annotation at ExPASy 
The tree may be re-rendered at any time, and the following parameters may be changed:

Colour: the new colours may be selected in the colour tree
Width: the width of the generated image in pixels
Height: the height of the generated image in pixels
Font Size: the font size of the text on the generated image
True Branch Length: this will render the tree with equal length branches 
if turned off
Omit Delimiter: this will remove the accession identifier used to look 
up the protein in the database: i.e. if this field is checked and the identifier 
is of the form  12345/MY_PROTEIN it will be represented as "MY_PROTEIN" in the 
tree.
Delimiter: if you choose to provide additional text after the protein id in the
leaf nodes of the tree, a one character delimiter may be specified: for example

You can right click on the image at any time and select Copy SVG. You 
then paste the image into an image editing program such as Microsoft Paint, then 
from there Save As an image type such as JPEG or GIF which may be imported into
PowerPoint or Word.