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MorphoBank recognizes that Nexus format allows and TNT formats allow the user to distinguish between polymorphisms and ambiguities uncertainty for multistate taxa.

Under the Preferences in the Matrix Editor, the user can select whether to treat multistate taxa as "polymorphic" or "uncertain". The default condition is "polymorphic". This choice applies matrix-wide but can be modified on a per-cell basis using the cell editor. Changing a selection in the cell editor affects only that cell.

The multistate taxa tool will be grayed out (disabled) if only one state has been scored for a given cell.

For display purposes on screen in the MorphoBank matrix editor, multistate taxa that are scored as polymorphic by the user appear as separated by a comma, like this "0, 2". Multistate taxa that are scored as uncertain by the user appear as separated by a slash, like this "0/2" or this "1, 4, 6"

The underlying Nexus or TNT file that MorphoBank produces will download such that a cell containing multistate taxa that are polymorphic will be represented as "{0, 2}" in the Nexus or TNT file, and multistate taxa that are uncertain will be represented as "(0, 1)".

If a pre-existing Nexus or TNT file contains the distinction of polymorphic vs. uncertain multistate taxa and is loaded to MorphoBank, the distinction will be preserved and will display as such. Any new changes to the matrix that the user enters will be preserved in future downloads.

Labels

How

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does the image labeling features work?

How to use the image viewer

Use the mouse to click and drag across the image. You can use the mousewheel or trackpad to zoom in or out of the image. The + and - buttons and zoom slider bar at the top of viewer may also be used. The viewer displays the image at full resolution, loading detail as you zoom. The more you zoom the more detail will be visible.

You may annotate the image with text notes. Each annotation is associated with a point or rectangular area of the image. To create an annotation, select the line (point) or rectangle tool from the tool bar, then click on the location you wish to annotate. For point annotations a line will appear connecting the location with a text box. You may drag both the point of the line and the text box to adjust position. Click on the text box to add text. For rectangular annotations a rectangle will appear. Drag on the edges at the highlighted locations to resize the rectangle. Drag the rectangle on its interior to reposition it. You may also drag the text box into position. Click on the text box to add text. All changes to annotations are saved automatically as you work.

Toolbar guide

When this tool is selected clicking and dragging on the image will pan across it.

When this tool (or the six-sided polygon) is selected, clicking on the image will add rectangular labeled regions at a location. You can resize the region by clicking and dragging on the drag points. Click and drag on the center of the region to relocate the region.

When this tool is selected clicking on the image will add labels to associated with point locations. The area around the point location will be highlighted with a light transparent red circle. Click and drag within the circle to move the label.

You can see an overview of the entire image, with the currently visible area highlighted by clicking on this tool. Clicking on a point in the overview will pan the magnified image to that location.

You can use this button to prevent accidental movement or deletion of labels while navigating the image. When locked it will not be possible to move, editing, create or delete labels on the image. You can still use the zoom and pan tools when the labels are locked.

You can zoom out to fit the entire image, centered, in the viewer window by clicking on this tool.

Keyboard shortcuts

Single-key shortcuts are available for common actions. Pressing the key is equivalent to the corresponding mouse action.

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How can I be sure my data is secure?

Another An advantage of a web-based system like MorphoBank is that time-consuming maintenance tasks such as data backup can be centralized. MorphoBank runs on servers hosted by the State University of New York at Stony Brook. All data on the main MorphoBank server at Stony Brook is backed up to tape, as well as to off-site mirror servers at the American Museum of Natural History. Stony Brook servers are backed up nightly and serviced by a professional full-time staff of system administrators. Currently the Stony Brook backup system is scheduled to run nightly incremental backups.

If disaster should strike we should be able to recover virtually all lost data. For data recovery, the Morphobank system administrator will work with the Stony Brook system administrators to get the data loaded back in to the MorphoBank Portal.

For optimal security we suggest you perform your own periodic back-ups using the project "download" feature. This can be found on the right side of the project overview page (the summary page displayed when you first select a project) and will provide you with a Zip-format archive containing all matrices and media from your project.

Note that a project download is not a full backup in that it can not be reloaded into MorphoBank to reconstitute a project. The download consists of separate NEXUS files and images. Media, characters, taxa and scoring are all retained, but labels and links between matrix characters and cells to media will not be retained due to limitations in the NEXUS file format. Thus we do not recommend deleting your work within MorphoBank unless you are absolutely sure you no longer need your project.

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