• Manuals

Browse the manual

• Introduction to the Phylogeny Module
  • Phylogeny
  • Features
• System requirements and installation of the Phylogeny Module
  • System requirements
  • How to install a plug-in
  • How to uninstall a plug-in
• Alignment of sequences
  • Create an alignment
    • Gap costs
    • Fast or accurate alignment algorithm
    • Aligning alignments
    • Fixpoints
  • Join alignments
    • How alignments are joined
  • Pairwise comparison
    • Pairwise comparison on alignment selection
    • Pairwise comparison parameters
    • The pairwise comparison table
• Create Trees
  • K-mer Based Tree Construction
  • Create tree
  • Model Testing
  • Maximum Likelihood Phylogeny
  • Bioinformatics explained
    • Substitution models and distance estimation
    • K-mer based distance estimation
    • Distance based reconstruction methods
    • Maximum likelihood reconstruction methods
    • Bootstrap tests
• Tree Settings
  • Minimap
  • Tree layout
  • Node settings
  • Label settings
  • Background settings
  • Branch layout
  • Bootstrap settings
  • Metadata
  • Node right click menu
• Metadata and Phylogenetic Trees
  • Table Settings and Filtering
  • Add or modify metadata
  • Selection of specific nodes
• Bibliography

How to install a plug-in

Plug-ins are installed using the plug-in manager^2.1:

        Help in the Menu Bar | Plug-ins and Resources... ()

   or  Plug-ins () in the Toolbar

The plug-in manager has four tabs at the top:

• Manage Plug-ins. This is an overview of plug-ins that are installed.
• Download Plug-ins. This is an overview of available plug-ins on CLC bio's server.
• Manage Resources. This is an overview of resources that are installed.
• Download Resources. This is an overview of available resources on CLC bio's server.

To install a plug-in, click the Download Plug-ins tab. This will display an overview of the plug-ins that are available for download and installation (see figure 2.1).

Figure 2.1: The plug-ins that are available for download.

Clicking a plug-in will display additional information at the right side of the dialog. This will also display a button: Download and Install.

Click the Phylogeny Module and press Download and Install. A dialog displaying progress is now shown, and the plug-in is downloaded and installed.

If the Phylogeny Module Plug-in is not shown on the server, and you have it on your computer (e.g. if you have downloaded it from our web-site), you can install it by clicking the Install from File button at the bottom of the dialog. This will open a dialog where you can browse for the plug-in. The plug-in file should be a file of the type ".cpa".

When you close the dialog, you will be asked whether you wish to restart the CLC Genomics Workbench. The plug-in will not be ready for use before you have restarted.

Footnotes

... manager^2.1

In order to install plug-ins on Windows, the Workbench must be run in administrator mode: Right-click the program shortcut and choose "Run as Administrator". Then follow the procedure described below.