Intreeactive help

How do I...

Zoom and pan around the tree?

To zoom in to a region of interest, click and drag to select that region.

To zoom in/out on the x-axis only, use the "X+" / "X-" buttons.

To zoom in/out on the y-axis only, use the "Y+" / "Y-" buttons.

To reset the zoom, either click the "Reset" button, or double click the tree.

Hovering over the bottom edge of the tree changes the cursor to a double arrow. Click and drag to scroll the x-axis left or right - the same is possible for the y-axis by hovering over the left hand edge of the tree.

Alternatively, by hovering at the top right corner of the tree the tool cluster becomes visible. Select the "pan" tool. It is then possible to click and drag to freely pan aroud the tree. To switch back to normal operation, instead select the "box select" tool.

Colour tips by metadata?

Tips on the tree can be coloured by associated metadata - the dropdown at the top-right corner of the tree can be used to select which field is used.

Show labels on the tips of the tree?

Tip labels can be enabled by clicking "Show labels". By default these show "ID", but by clicking the "Label by" dropdown this can be changed to any available metadata fields.

To show multiple metadata fields in the tip labels, for example - ID and date, select the first field from the "Label by" dropdown then click "+". Repeat this for each additional field to be added.

To remove a field from the label, hover over it and click to delete it. If all fields are deleted, the label will be whichever field is in the dropdown menu as per normal operation.

Search for a particular ID?

To search for tip IDs, enter your query into the "Highlight by ID" box. All matches will be highlighted on the tree in red.

Note, if zoomed in, some highlighted IDs may be outside the frame. Reset the zoom to ensure all matches are visible.

Click "clear" to reset the highlight.

Get detailed information about a tip on the tree?

Hovering over a tip on the tree displays detailed metadata associated with that tip.

This metadata is also visible by searching for the ID in the "Seach and compare metadata" section.

Click the underlined "ID" to highlight the corresponding tip on the tree.

Find the nearest neighbours for a particular ID?

By default, the nearest neighbours for an ID are displayed in the "Search and compare metadata" section. This finds the minimum number of SNPs to a neighbour, then displays all neighbours within that SNP distance.

In this example, there are 4 neighbours - a count is given at the top. The number of SNPs is 2 - indicated to the right of the ID.

Clicking an ID will highlight it on the tree. Selecting the "Highlight all" button will highlight the sequence of interest and its nearest neighbours.

Use my own custom SNP threshold for nearest neighbours?

By default, the minimum number of SNPs to a neighbour is used - this is the "Use min" option.

To set a custom threshold, select "Set manually" and enter the number of SNPs to use in the box to the right of this.

If the custom threshold is lower than the minimum, "No neighbours within threshold" will be displayed in the "Search and compare metadata" section.

Download an image of the current view?

To download a snapshot of the current tree view, hover of the top-right corner of the tree. The "download plot" tool becomes visible.

Clicking this will save an image of the current view.