Creating phylogenetic tree in Genome Workbench from a multiple alignment
For fast/rough tree construction use newly created multiple alignment, or upload alignment (in Fasta format) created previously (using File -> Open -> select File Import, for File Format select FASTA Alignment files, browse to your file and click Next/Next/Finish) into new project.
Select multiple alignment file in the Project view, open Tools dialog, select Phylogenetic Tree Builder Tool, and click Next:
In the “Run Tool – Phylogenetic Tree Builder Tool” dialog select alignment (if not selected by default), and select Distance Method (Poisson (protein), Kimura (protein) or Jukes Cantor (DNA)), Tree Construct Method (Neighbor Joining or Fast Minimum Evolution) and Labels for Leaf Nodes representation, and click Finish.
Wait for tree construction (might take a few minutes, depending on the alignment size). Find newly created tree and distant matrix added to the project:
Select Tree file in the project view and open in Tree View.
Tree opens at zoom 0:
Open right click menu and see set of options that can be used for tree manipulation. For our tree we used: layout - rectangle cladogram, zoom behavior - vertical, re-root - set midpoint root. For the leaf node labels we select settings/labels/custom labels using properties and set up $(label)__$(organism) in this “Properties” dialog:
For complete set of tree manipulation/editing options see Using Tree View tutorial.
Pease also see the Phylogenetic Trees Video tutorial.
In tree view, zoom in to the level where individual labels are seen and see custom labels:
Current Version is 3.8.2 (released December 12, 2022)
General
Help
Tutorials
- Basic Operation
- Using Active Objects Inspector
- Configure tracks and track display settings
- Working with Non-Public Data
- Viewing Multiple Alignments and Trees
- Broadcasting
- Genes and Variation
- Generating and Viewing Sequence Overlap Alignment
- Working with BAM Files
- Loading Tabular Data
- Working with VCF Files
- Sequence View Markers
- Opening Projects in Genome Workbench
- Publication quality graphics (PDF/SVG image export)
- Editing in Genome Workbench
- Create Protein Alignments using ProSplign
- 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
- Searching in Genome Workbench
- Graphical View Navigation and Manipulation
- Using the Text View to Review and Edit a Submission
- BAM haplotype filtering
- Displaying new non-NCBI molecules with annotations
- Creating phylogenetic tree from precalculated multiple alignment
- Creating phylogenetic tree starting from search
- Video Tutorials
General use Manuals
- Tree Viewer Formatting
- Tree Viewer Broadcasting
- Genome Workbench Macro
- Query Syntax in Genome Workbench and Tree Viewer
- Multiple Sequence Aligners
- Running Genome Workbench over X Window System
NCBI GenBank Submissions Manuals
- Table of Contents
- Introduction
- Genome Submission Wizard
- Save Submission File
- Reports
- Import
- Sequences
- Add Features
- Add Publication
- Comments
- Editing Tools