HomeCLC FAQ - Analyses-related questionsPhylogenetic treesHow to save the decorations on a phylogenetic tree?

11.1. How to save the decorations on a phylogenetic tree?

When decorating, a phylogenetic tree using the options in the side panel the decoration information is not saved to the file of the phylogenetic tree, as all the decorations options in the side panel are only view settings. It is certainly possible to save the view settings for a phylogenetic tree. When saving the view setting of a tree you can select whether you want to apply the view settings for only the phylogenetic tree that you are currently working with or if you would like to save the settings for tree views in general.

The advantage of using view settings instead of saving the decorations to the actual phylogenetic tree file are:

  • The option to save and apply the different decorations to different phylogenetic trees
  • The option to save different view settings e.g. cladogram with red diamond shaped nodes, phylogram with bootstrap value etc. and then quickly apply these setting to different trees by only clicking two buttons
  • The option to choose to automatically show you favorite layout using the Use as Standard view settings for tree view option (described below)

 

1. To save and apply your view settings on a specific phylogenetic tree please:

  • Select the view settings that you prefer in the side panel
  • Click on the Save View... button in the lower right corner of the workbench (Figure 1)
  • Enter a name for the view settings in the text box (Figure 2)
  • Click the Save button to save the view settings
  • Click the Close button to close the window
  • Save the phylogenetic tree

After saving the view settings in this way, they will automatically be applied the next time that you open the phylogenetic tree.

 

Figure 1. Click on the Save View... button to save view settings.

 

 

Figure 2. Enter a name for the view settings and press Save.

 

 

 

2. To save your view settings on phylogenetic trees in general please:

  • Select the view settings that you prefer in the side panel
  • Click on the Save View... button in the lower right corner of the workbench (Figure 1)
  • Enter a name for the view settings in the text box
  • Check the Save for all tree views check box (Figure 3)
  • Click Save button to save the settings
  • Click the Close button to close the window

 

Figure 3. Save the view settings for application to other trees.

 

 

 

3. To apply Saved View Settings to a phylogenetic tree please:

  • Open the phylogenetic tree
  • Click on the Save View... icon in the lower right corner of the workbench
  • Select the saved view setting to apply from the drop-down list and click the Apply button (Figure 4)
  • Click Close button to close thewindow

The saved view will now be applied.

 


Figure 4. Select which saved view to apply or to revert to the CLC Standard Settings.

 

 

 

4. Customize the standard view settings for phylogenetic trees

  • Create and save view settings as described in section 2, but don't close the window
  • Select the saved view setting to apply from the drop-down list
  • Check the Use as standard view settings for a tree view check box (figure 5)
  • Click the Apply button
  • Click the Close button to close the window

The view will now be used for all phylogenetic trees.

 

Figure 5. Customize the standard settings using the option Use as standard view settings for a tree view

 

 

 

5. To Remove Tree View Settings please:

  • Open the phylogenetic tree
  • Click on the Save View... button in the lower right corner of the workbench
  • Select the view to removefrom the drop down list in the lower part of the window
  • Click the Remove button (Figure 6)
  • Click the Close button to close the window

 


Figure 6. Select the view settings that you would like to remove again.

 

 

For more information about Saving, applying and removing saved settings please see the manual following the links below:

CLC Main Workbench:

http://resources.qiagenbioinformatics.com/manuals/clcmainworkbench/current/index.php?manual=View_settings_Side_Panel.html

CLC Genomics Workbench:

http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=View_settings_Side_Panel.html

Biomedical Genomics Workbench:

http://resources.qiagenbioinformatics.com/manuals/biomedicalgenomicsworkbench/current/index.php?manual=View_settings_Side_Panel.html

 

 

For more information about Phylogenetic trees please see section following the links below:

CLC Main Workbench:

http://resources.qiagenbioinformatics.com/manuals/clcmainworkbench/current/index.php?manual=Phylogenetic_trees.html

CLC Genomics Workbench:

http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Phylogenetic_trees.html

 

You might also be interested in our tutorial on visualization of trees, which you can find here:

http://resources.qiagenbioinformatics.com/tutorials/Phylogeny-module-visualization-of-Trees-and-Metadata.pdf

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