Analysis view

The Analysis view shows tracks for a single sequence. The view is empty or cannot be opened at all unless the session contains only one sequence; or until a single sequence has been chosen in the Overview or Explorer panel, or by using the navigation tools or Places panel bookmarks. At that point, the Analysis view appears automatically and is populated with data.

To access the Analysis view at any time, click on the Analysis tab, the dark blue tab in the image below, or use View > Analysis.

By default, the Analysis view displays a header and footer, along with a sequence and its corresponding data tracks. Tracks in the Analysis view can have different appearances depending on the zoom level.

The following table shows tasks associated with the Analysis view:

Task	How To
Display the search tools	To display the search tools in the upper left of the Analysis view, use the Find tool ( ).
Sort constituent sequences	To sort read files (the files in the left margin of the view) according to the selected criteria, use the Sort reads tool (). By Name – Sorts read files in alphanumeric order by name. This type of sorting is normally only used for Sanger reads, which are often user-named. This is a shortcut to the Sequence > Sort Reads > By Name command. By Position – Sorts read files by their position along the consensus. This is a shortcut to the Sequence > Sort Reads > By Position command. By Variant – Brings all the reads containing variant bases to the top of the alignment stack. This is a shortcut to the Sequence > Sort Reads > By Variant command. When you choose this option, SeqMan Ultra automatically loads and calculates the SNPs. Note that if you are working with a large .sqd project, this calculation can take a considerable amount of time.
Adjust the zoom level	Use the Compact text tool () to adjust the zoom level to maximize the number of bases while keeping the text legible. Use the Restore default zoom tool () to adjust the zoom level to the (wider) default setting, making the text more comfortable to read.
Export data	Use the Export data tool () and choose between Export Aligned Sequences and Export Consensus. This tool acts as a shortcut to the File > Export Data > Aligned Sequences and File > Export Data > Consensus commands and opens the same popup dialogs. See Export data to a file for information on using the dialog.
Export image	Use the Export image tool (). This tool acts as a shortcut to the File > Export Image > Analysis command. See Export an image of a view for more information.
Change the color scheme, font, or layout	Use the Style panel’s Sequence section and/or Analysis section.
Show/hide the header & footer	Click on the small dark gray arrows near the upper right corners of each section.
Show a vertical guideline	Click Analysis > Show Guideline. The presence of a check mark directs GenVision Pro to display the guideline. A vertical guideline is displayed by default, and is a navigational aid to help in guiding your eye between sequences and tracks.
Hide a vertical guideline	Click Analysis > Show Guideline. The absence of a checkmark means that only an abbreviated version of the guideline will remain visible in the header and footer.
Save a location of interest	Choose Analysis > Add Place to Favorites or right-click within the Analysis view and choose Add Place to Favorites. The following popup appears. The popup shows the selected coordinates. You can keep the coordinates as the name or overwrite them with a different name. Press OK.