build and customize phylogenetic trees › brcdocs › tutorials › ... · build and customize...
TRANSCRIPT
http://www.fludb.org/
Freely available Integrated datasets Bioinformatics tool suite Platform for influenza data submission
IRD is funded by the National Institute of Allergy and Infectious Diseases (NIH/DHHS) under Contract No. HHSN266200400041C and is a collaboration between Northrop Grumman Health IT, University of Texas Southwestern Medical Center , Vecna Technologies, SAGE Analytica and Los Alamos National Laboratory. Comments, questions, suggestions? Contact us at [email protected]
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. Identify nucleotide sequences to include in the phylogenetic tree analysis: mouse-over the “Search Data” tab and click “Nucleotide Sequences”. For flu, we recommend you use nucleotide sequences for phylogenetic analysis unless you are analyzing widely divergent sequences.
2. Choose search criteria on the Nucleotide Sequence Search page and click the “Search” button to run your search.
3. 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”.
4. On the Generate Phylogenetic Tree page, choose parameters and click “Build Tree”.
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Click to view details of
the record
• Select display fields • Custom-sort records
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.
2
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http://www.fludb.org/
Freely available Integrated datasets Bioinformatics tool suite Platform for influenza data submission
IRD is funded by the National Institute of Allergy and Infectious Diseases (NIH/DHHS) under Contract No. HHSN266200400041C and is a collaboration between Northrop Grumman Health IT, University of Texas Southwestern Medical Center , Vecna Technologies, SAGE Analytica and Los Alamos National Laboratory. Comments, questions, suggestions? Contact us at [email protected]
Option 2: Use a working set or upload your own sequences and then build a phylogenetic tree
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1
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. For flu, we recommend you use nucleotide sequences for phylogenetic analysis unless you are analyzing widely divergent sequences.
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
Use nucleotide sequences unless you are analyzing
widely divergent sequences.
Three options to input sequences 3
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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