Using Tree View
Introduction
This tutorial will serve as a consolidation space for all existing help on using Tree View in Genome Workbench.
Step 1: Adding a Phylogenetic Tree View
The same way you open different types of views for your project - you can add a Phylogenetic Tree.
Step 2: Explore Pylogenetic Tree View Features
Phylogenetic Tree View offers the users multiple features.
Users can:
- Set layout options
- Perform search
- Display distances
- Manage labels
- Set markers to highlight nodes
- Set subtree boundaries
- Load attributes
- Reroot tree
More information can be found in the Tree Viewer formatting manual.
Step 3: Arranging Windows
In order to experience interactions between different views the user can arrange windows with different views
Step 4: Tree View Interactions with other Views
Tree Views supports broadcasting between phylogenetic tree views.
It can also interact with other views
Step 5: Saving Tree View as a PDF file
Tree View can be saved in PDF format for printing or other presentation needs.
Step 6: Online Tree Viewer
Some of the features of Genome Workbench Tree View can be experienced by using the online tool Tree Viewer.
Current Version is 2.12.5 (released September 18, 2017)
Downloads
- FTP site for all downloads
- Windows
- Mac OS X 10.8+ (Mountain Lion, Mavericks, Yosemite)
- Linux (Ubuntu 16.04 "Xenial Xerus")
- Linux (OpenSUSE Leap 42.2)
- Linux (Fedora 26)
- Linux (Fedora 25)
- Linux (Debian 9 "Stretch")
- Linux (Debian 8 "Jessie")
- RPM Installation key
- Source
- Older Versions
General
Help
Tutorials
- Basic Operation
- Using Active Objects Inspector
- Working with Non-Public Data
- Working with Multiple Views
- Broadcasting
- Genes and Variation
- Generating Sequence Overlap Alignments
- Working with BAM Files
- Loading Tabular Data
- SNP Table View
- Sequence View Markers
- Projects and Workspaces
- Publication quality graphics (PDF image export)
- Create Protein Alignments using ProSplign
- Exporting BAM/cSRA Coverage Graphs as WIG Files
- GFF-CIGAR export for alignments
- Exporting Tree Nodes to CSV
- Generic Table View
- Running BLAST search against custom BLAST databases
- Using Phylogenetic Tree
- Coloring methods in Multiple Alignment View
- Displaying translation discrepancies
- Graphical View Navigation and Manipulation
- Video Tutorials
Manuals
- Tree Viewer Formatting
- Tree Viewer Broadcasting
- Genome Workbench Macro
- Query Syntax in Genome Workbench and Tree Viewer
- Multiple Sequence Aligners