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: