ViPR is funded by the National Institute of Allergy and Infectious Diseases (NIH / DHHS) under Contract No. HHSN272200900041C and is a collaboration between Northrop Grumman Health IT, University of Texas Southwestern Medical Center and Vecna Technologies. Comments, questions, suggestions? Contact us at feedback@virusbrc.org

Build and Customize Phylogenetic Trees

• Options to select and optimize evolutionary models • Customize tree display, rooting, subtree arrangement, tree tip labels, tree leaf coloring, etc. • Export a publication quality tree image

Option 1: Search for sequences and then build a phylogenetic tree

Choose sequence data for the tree tool

Calculate phylogenetic relationships

Decorate the tree based on your needs

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4

• Run ModelCompare to see which evolutionary model best fits your data

• Set your own parameters for a certain model

• Choose a tree algorithm: PHYML or RAXML

Customize tree tip labels

1. On the ViPR homepage, choose a virus family to start. 2. Identify sequences to include in the phylogenetic tree analysis: mouse-

over the “Search Data” tab and click “Genomes” or “Genes & Proteins”. For this example, we will use genome sequences.

3. Choose search criteria on the Genome Search page and click the “Search” button to run your search.

4. Select sequences from the search result page by clicking the checkboxes. Mouse-over the yellow “Run Analysis” button, and click “Generate Phylogenetic Tree”. If you want to include sequences that are not in this search result, select desired sequences and click “Add to Working Set”, then add additional sequences to the same working set. Click the “Workbench” tab, find the working set you saved and click

next to it. On the working set details page, mouse-over “Run Analysis” and click “Generate Phylogenetic Tree”.

5. On the Generate Phylogenetic Tree page, choose parameters and click “Build Tree”.

http://www.viprbrc.org/

Freely available Integrated datasets Bioinformatics tool suite

1

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3

Select sequences and add them to a working set for future analysis.

You’ll need to register for a Workbench account to

use this feature.

• Select display fields • Custom-sort records

Click to view details of

the record

2

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Option 2: Use a working set or upload your own sequences and then build a phylogenetic tree

1. Mouse-over the “Analyze & Visualize” tab and click “Generate Phylogenetic Tree”.

2. On the Generate Phylogenetic Tree page, choose “Quick Tree” to use default parameters or click “Custom Tree” to set your own parameters.

3. You have three options to input your sequences:

3.1 Upload a FASTA- or Phylip-formatted file. 3.2 Paste sequences in FASTA or Phylip

format. 3.3 Use a working set from your Workbench. Choose the format of sequences you

provided. Then click “Build Tree”.

2

3.1

Three options to input sequences

3

3.3

• Run ModelCompare to see which evolutionary model best fits your data

• Set your own parameters for a certain model

• Choose tree algorithm: PHYML or RAXML

Customize the look of the tree

1. After the tree analysis is finished, click “View Tree” to load the Tree Viewer window.

2. A tree viewer window will pop up – see screenshot to the left.

3. Many tree customization options exist: • Click the node of a reference point to

reroot the tree • Collapse/expand/display subtree • Swap descendants • Choose tree decoration options to

custom-color tree leaves • Resize the tree • Change tree type: rectangular,

circular, unrooted, etc. 4. Download the tree image/legend

from the “File” menu.

Choose the format of sequences

Export tree to PDF/PNG/JPG file

Click to color tree based on strain characteristics

Resize the tree

View phyloXML/ Newick/NHX/Nexus file

Change tree layout: rectangular, circular, etc.

Options for display/ search/graphics export

options

Click the respective node to: • Reroot the tree using a

reference point/outgroup • Display node data • Collapse/expand subtree • Display subtree • Swap descendants

Search for text in labels

http://www.viprbrc.org/

Freely available Integrated datasets Bioinformatics tool suite

ViPR is funded by the National Institute of Allergy and Infectious Diseases (NIH / DHHS) under Contract No. HHSN272200900041C and is a collaboration between Northrop Grumman Health IT, University of Texas Southwestern Medical Center and Vecna Technologies. Comments, questions, suggestions? Contact us at feedback@virusbrc.org

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3.2