PhyloView Tutorial

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
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
  1. Open the PhyloView tool (link will open in new window).
  2. 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.
  3. 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.
  4. 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.
  5. 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
  6. 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
  7. 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.