The following table describes components of the MegAlign Pro user interface, along with links to more in-depth information about each item:
| Item | Description |
|---|---|
| Menus | The MegAlign Pro menus are: MegAlign Pro (available only on Macintosh), File, Edit, View, Align, Features, Sequences, Overview, Distance, Tree, Window and Help. Some menu commands can also be initiated by keyboard shortcuts, tools, and/or context menu (right-click) options. |
| Tools | The MegAlign Pro toolbar is situated just below the menus. To toggle between showing/hiding the toolbar, choose View > Show (Hide) Toolbar. |
| Projects | In MegAlign Pro, each project is displayed in a separate tab with an .msa extension. |
| Overview | The Overview provides a way to navigate within the sequences, no matter what type of sequences or alignment is used. In the case of Mauve-generated alignments consisting of multiple alignment blocks, the Overview also allows you to explore the relationships between aligned blocks. |
| Sequences view | The Sequences view shows the sequences and any enabled tracks (see Work with Tracks). |
| Distance view | The Distance view, available only after an alignment has been performed, shows a matrix (i.e., table) of numbers representing distances between each pair of sequences for the alignment block selected in the Overview. Sequence distances are used as input in creating the Tree View. In the case of multi-block alignments, each alignment block will have a separate matrix. |
| Tree view | The Tree view, available only after an alignment has been performed, shows evolutionary relationships predicted from the multiple sequence alignment, and is calculated using the current Distance metric. In the case of multi-block alignments, each alignment block will have a separate tree. |
| Panels | The Style, Tracks, Features, Places and Details panels allow you to specify how to display items in the views, or show details about items in the views. |
| View splitter | The view splitter is used to divide the Sequences view or Overview vertically into multiple panes. |
| Header/footer | A header and footer are collapsible sections above and below the selected reference sequence. They contain tracks that apply to all those sequences and their alignment, if any. The Overview provides a header, and the Sequences view provides a header and footer. |
| Sequence ruler | Sequence rulers pertain only to the sequences just above them, and use pre-alignment (ungapped) numbering. Gaps are not counted in this ruler. |
| Show/hide icons | The gray circles to the left of each sequence name in the Sequences view and Overview contain a plus or minus sign. These toggle between displaying and hiding the detail tracks. |
| Console | The Console panel displays information about an alignment in progress, or a log for a completed alignment. |
| Console toolbar | This toolbar is located in the upper right of the Console and pertains only to the Console. |
Need more help with this?
Contact DNASTAR