Tree Data

Tree File Formats

• Newick format (.nwk, .newick, .tre, .nhx, .tree, or .treefile)

• Nexus format (.nex or .nexus)

SNPs in the tree file need to be represented as numbers to reflect the branch lengths.

Tree Data Configuration

File

Within the tree panel configuration panel, a local tree file or network location (URL) can be specified.

Labels column

In addition, the column in the metadata table that contains the leaf labels must be specified. The tree data must relate to the metadata table, so the tree file must contain a column containing values matching values in one of the metadata columns, which is selected here as the Labels Column. The column can have any name; the requirement is only that the values in that Labels Column must be in the tree file.

Hide data without matching tree leaves

There is also an option to "Hide # data entries without matching tree leaves."

This toggle appears in the Edit Panel: Tree interface when there are rows in the metadata table that do not have matching entries in the Tree File. Toggling this on removes the metadata rows that don't have a match, so that those rows are no longer part of any of the panels.